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What other improvements would you like to see on the UCSC Genome Browser?
#Response DateComment
1.Thu, 4/26/07 3:35 PMYour interface is so easy to use, I'd like to see all genomes that are sequenced accessible, including plants.
2.Thu, 4/26/07 5:24 PMA very useful feature would be a more convenient way to save custom tracks for more than a day. E.g. through user-specific accounts (which would also make it possible to retrieve them from a different computer). If server space doesn't permit that, an alternative would be a feature that makes it possible to download all my custom tracks at once into a single BED file, so they can be uploaded again later all at once. Right now custom tracks can only be downloaded one-by-one which is quite inconvenient when you have generated many of them in a session.
3.Thu, 4/26/07 5:24 PMI'd like a font that was a little bigger than the default, but a little smaller than the next available option.
4.Thu, 4/26/07 7:05 PMImproving the output of LIFT tool to include both the input and the output in one file. When one submit a list of positions and some failed it is unnedded hard to pair the transferd positions.
5.Thu, 4/26/07 7:29 PMImproved functionalities for integration of user annotation and data.
6.Thu, 4/26/07 9:26 PMrecently you made a change in the UCSC Known Genes display page for individual genes, which I wish you could undo and revert to the earlier version: you no longer present different refseq IDs for each individual 'UCSC known gene' in a given gene display. Instead you have decided to collapse multiple 'known genes' into a single refseq ID, and differentiate them by your own internal "UCSC ID". This has ramifications when designing primers using the ExonPrimer link for individual 'UCSC known genes' - the output of the exonPrimer file now lists the "UCSC ID", where before it listed the (different) individual refseq or genbank IDs. The net result is an extra layer of work in primer design, wherein I have to manually replace the UCSC ID with an "Alternate Gene Symbol", so as to distinguish in my primer design files between different 'UCSC known genes'.
7.Thu, 4/26/07 10:17 PMI find the browser to be non-intuitive. It takes too long to find the information I need. I think you need to work with some human computer interaction groups and users to improve the ability to find information.
8.Fri, 4/27/07 12:08 AM1) Novel gene track would be a great addition that can be part of a "Manually curated" gene set submitted by researchers with published work on novel genes. Each gene submission can come with its own information content such as author association, validation (in silico, experimental), expression data, genomic context (subtelomeric, near breakpoint boundary or another marker), non-coding regulatory regions on mRNAs, etc. One can restrict submission to a certain essential set of annotation features that need to be provided for each novel gene or RNA. 2) If you could make available the more detailed flat file databases, especially the ones that associate chromosomal range of every "bin" field--would be a big help. 3) UCSC MySQL database querying using remote connection--faster server support would be great. Thanks for all that you have provided already, Charu Gupta Kumar
9.Fri, 4/27/07 2:02 AM1) Given the large number of ESTs/mRNAs that can be present in a given genomic region, if there was a way to specify the number of ESTs or mRNAs that one wants to display in the "pack" mode--that would be really nice. E.g., in chrX:151,073,054-151,383,976, I should be able to specify in the configuration that I want to display only 20 ESTs, and 10 mRNAs. Then based on score, the top 20 ESTs can be displayed. It will ease many display and database access issues for a given screen display. 2) Not enough support for new features that get added--what are those colored lines at the end of mRNA/spliced ESTs, or exons??? Thanks.
10.Fri, 4/27/07 2:05 AMMore instructions on joining tables in order to make custom datasets as needed for a given project
11.Fri, 4/27/07 2:55 AMAbout Table Browser. Nice: easy and easily see MySQL table scheme. Bad: It may be difficult to get protein amino acid sequence. About Genome Browser. I'd like to see forward and complement strand at a time. I'd like to access genome-test MySQL server sometimes.
12.Fri, 4/27/07 9:28 AMIntroduce inverted repeat track finder
13.Fri, 4/27/07 10:25 AMcomprehensive blat documentation
14.Fri, 4/27/07 12:03 PM1. microRNAs - everything about them!! The current assembly still doesn't have the tracks for targets! 2. Mouse polymorphisms Vs strains. Most of this can be readily added from MGI. 3. Better representation of the putative cis regulatory regions (conserved TFBSs).
15.Fri, 4/27/07 12:15 PMThe ability to point and click zoom in to specific regions of a chromosome, rather than scrolling up and down.
16.Fri, 4/27/07 4:45 PMajax interface :-), no seriously: more orthology information for proteins
17.Fri, 4/27/07 8:21 PMMake drop down tables in the table browser more user-friendly.
18.Fri, 4/27/07 8:22 PMI would like to be able to specify the size of the image in the .PS files. I would like to be able to combine my custom tracks to a single entiety Please write clearer descriptions for how to do things, i.e. custom tracks The descriptions are often hard to follow and often require getting help from someone who has figure out how to do things. Overall, the browser is a superb resource. I have started to include it in the courses that I teach. Thank you
19.Fri, 4/27/07 8:37 PMI wish that when I type something wrong in the search box that instead of returning me some random data for Chromosome 12 with a small notice at the top that says,"Sorry couldn't locate xyz in the genome database", that it would be a bigger red notice that would pop up and maybe flash once or twice!
20.Fri, 4/27/07 8:50 PM1. Make custom tracks from BLAT search hits, or excract BLAT hits in BED or other formats. 2. Make the BLAT search more flexible. For example, having options to select for the number of hits in the output. 3. Include plant genomes
21.Fri, 4/27/07 8:53 PM1. Make it easier to view genes in a 5' to 3' orientation from left to right at all levels of resolution. 2. Allow the user to customize which tracks appear so that less-often used tracks do not obscure the interface. 3. Is it possible to allow click-and-drag navigation like Google Maps instead of the crude left and right arrow buttons? 4. Allow users to zoom on exons easily to see reading frames and translation products.
22.Fri, 4/27/07 8:54 PMThe browser does a really good job. it would be nice to have a simpler way to download lists of gene predictions for regions, preferably retaining links to additional data.
23.Fri, 4/27/07 8:59 PMIt would be good to keep all your tracks available when a new assembly is released. For instance, I'm always using the previous mouse assembly because I'm interested in the CAGE data and it is not displayed on the current assembly.
24.Fri, 4/27/07 9:01 PMUpdate all tracks for the latest build (such as the SNP and copy number polymorphism tracks).
25.Fri, 4/27/07 9:02 PMSupport compressions when uploading custom tracks. More flexibility/convenience in customizing existing tracks and beutify them for display(easier/faster to reorder, expand individual tracks, ability, ability to make the background vertical lines less prominent for print purposes). Ability to display gene tracks with less redundancy (ie. show genes rather than transcripts).
26.Fri, 4/27/07 9:07 PMDo more than one intersection with the Table Browser ie, intersect 3 or more tables. Also to be able to limit the intersection to the amount of elements that occur: ie, if I'm intersecting my binding site BEDs with my promoter BEDs, I'd like to ask for an output with promoters that have one intersected item (ie, one site in that promoter BED), 2 items, 3 items, etc (ie, there were 2 binding site elements within that specific promoter BED, etc)
27.Fri, 4/27/07 10:37 PMhorizontal scrolling should be dynamic (like google maps) you should be able to place multiple vertical cursor lines so that features in different tracks can be easily compared. you should be able to place vertical cursor lines to delimit zoom-in range
28.Fri, 4/27/07 11:24 PMimprove the table browser for interactive summary analysis and data mining
29.Sat, 4/28/07 12:00 AMHow about seeking collaborations around the world to set up more mirror sites?
30.Sat, 4/28/07 1:48 AM1- After experimenting with all three genomic web sites, I have come to use the UCSC one the vast majority of the time. I really think you have the format that puts the most information in the least graphical space, while conveying the most information. You make the point that sometimes a black and white film beats the Technicolor versions (even if you are too young to know what Technicolor was). Bravo, Guys and Gals. Bravo! 2- I am interested in doing promoter comparisons among genes within species and cross species, in an attempt to locate shared binding sites for transcription factors. There are programs that do this, and for some of them one is asked to input gene names in various different ways. It would be useful to collect as many different database cross references as possible in one place -- Unigene cluster -- Entrez gene number -- official mouse gene name -- Swiss Prot -- Ref seq -- and also the same data for the same gene in other species via some type of link or pointer or something. Perhaps this is already here (obviously some of it is) but it often seems that some particular cross reference is missing, and that happens to be the one that is needed. But, once again, you can not imagine how grateful I am, as a typical end user, to have this site so readily available and so well presented.
31.Sat, 4/28/07 3:10 AMThe Genome Graphs should display more data types, including BED and WIG formats, and should have enhanced visibility for what it disiplays.
32.Sun, 4/29/07 2:46 AMUser ability to eliminate appearance of tracks that are never used, i.e. to keep them on the configure page but not on the browsedr page.
33.Sun, 4/29/07 4:12 AMto be able to see my blat sequence! I can see every other sequence (mRNA, EST, genomic) if I'm zoomed in enough, but I can't compare it to my input!
34.Sun, 4/29/07 1:35 PMAllow sharing of cusom made tracks: this can save a lot of resources and can be easily implemented by assigning a secret id for uploaded tracks and allowing sharing of this id by collaborators.
35.Sun, 4/29/07 3:04 PMMore ncRNA genes! Preferably with structure annotation.
36.Sun, 4/29/07 7:18 PMIm not sure why but it seems like my user settings get very confused when i jump between several species in a session. That is my only issue. Thanks
37.Sun, 4/29/07 11:52 PMJavascript. Reloading the browser every time for zooming takes unnecessary time and is really outdated. Also, personalized browsers would be good - right now there are so many tracks in the human browser that it's hard to find even the ones you know are there. And get Robert B to run his pseudogene program on all species - it's better than anything out there When will the paper be out? ;-).
38.Mon, 4/30/07 6:13 AMThere are specific issues regarding compatibility among browsers (Firefox vs IE).
39.Mon, 4/30/07 7:17 AMPlease add & insect genomes (& update those you have). Eg honey bee, soon: nasonia, Triboliuem...
40.Mon, 4/30/07 7:28 AMdirect links between UCSC browser and other useful databases such as the HapMap site and genome variation database. For example, currently the links for SNPs are to dbSNP, which is not very useful.
41.Mon, 4/30/07 8:28 AMMultiple alignments of fewer core mammalian species would be welcome e.g. human-dog-mouse-rat and one also including opossum. An easier method for reordering custom tracks.
42.Mon, 4/30/07 2:41 PMwish list for human and mouse genomes: - expression data in normal tissues from SAGE and MPSS data sets (in addition to microarray data). - tissue-specific CpG methylation data. - SNPs between C57BL/6J and as many other mouse strains as is feasible. - a CpG content wiggle track in addition to the current GC percent track. - visualization of uploaded sequence traces via either (easier) A/C/T/G wiggle tracks or (harder) incorporation of graphical trace into GIF image produced by browser.
43.Mon, 4/30/07 2:45 PMI would be nice to use In-Silico PCR for searching RNAs since I really like it for genomic DNA PCRs
44.Mon, 4/30/07 5:45 PM- Some way to overcome the display limit for a track in certain cases (ESTs!!), i.e. by somehow collapsing redundancy, thus freeing space for more features to be displayed. - Display non-canonical splice-sites in UCSC genes, Refseq genes, mRNAs, spliced ESTs.
45.Mon, 4/30/07 9:48 PMA lot of the terms are very opaque--including dense, pack, squish, etc., and their effects are sometimes inconsistent. I would like to see this improved. I would also like to be able to view information about a track within the track browser, e.g., have a mouse over summary on each track in the configuration section. I also have no idea what the chain, net, and so on terms are, and can't really discern a meaningful distinction between them. You might consider removing them altogether so as to simplify the user experience. In general, exposing more popular tracks automatically, and disclosing more of them in an 'advanced' option would make the whole thing a lot easier. The table browser should not be separate from the graphical browser. If I want a track, I should be able to left-click, or something of the sort, and save it to disk in whatever form I want.
46.Mon, 4/30/07 9:52 PMa somewhat more feature rich and fluid interface to perform annotation intersections would be a plus, as would be a better set of gene IDs that reduces the number of distinct but 'redundant' alternative splice forms (i.e. many 'genes' have multiple 'known gene' ids that are only separated by an exon or two)...notwithstanding this is a complex problem some simple heuristic rules would really help to clean up the 'known gene' set.
47.Tue, 5/1/07 4:02 AMMore qInsert info in mRNA and EST tables. e.g if I want to reject mappings with at least one insert >5nt, I cannot do this because qInsert is the sum of all the inserts in the query. This is important because such inserts can look like alternative splicing, when they are not.
48.Tue, 5/1/07 4:47 AMI work in an epigenetics lab and would find it very useful to be able to BLAT and in silico PCR bisulfite treated DNA sequences, and have the results map back directly to the human genome.
49.Tue, 5/1/07 11:05 AMnothing special
50.Tue, 5/1/07 3:33 PMThe new dog genome seems to have worse gene annotations than the previous version - seems like that could be improved. I am not really a plant biologist, but sometimes do work with plant data. It would be GREAT if you had an Arabidopsis thaliana genome browser. Rice, wheat, and maize would also be nice additions. There's a lot of research to be done with plants (remember RNAi was discovered in plants), and I'm sure the plant community would use this resource. I've recently seen mouse gene annotation tracks from the Jackson Lab. It's good to have those on there, thanks!
51.Tue, 5/1/07 6:13 PMClones please, contigs are ok, but we have noticed some sequences are being lost on contig blast.
52.Tue, 5/1/07 11:10 PMDo you plan to implement AJAX in your browser, such that users can drag and move around the browser regions as they wish, instead of clicking the arrow button?
53.Wed, 5/2/07 5:58 AMTool for primer design that can distinguish between genomic DNA and cDNA (design for example primers over exon-exon borders for RT-PCR or over introns - show size of both PCR products from genomic and cDNA)... for sequence retrieval for genes: show exon intron stucture (exons in capital, all introns in small letters) - if this is not the case yet (I couldn't find it, only repeats in small letters... option)
54.Wed, 5/2/07 8:53 AMPosition zoom in/out button are only NUMx power. If we can zoom in/out numerical bp base, it may be so useful and handy.
55.Wed, 5/2/07 3:34 PMDon't fix what ain't broke. The main browser window, while not as polished as it could be, works very well and people are used to it. Please don't do what all these big websites do and reboot the whole thing from the ground up for the sake of getting a new look. We like it the way it is.
56.Wed, 5/2/07 5:32 PMThere used to be a function that allowed you to click on a feature on the left hand tab and a "line" would extend across the width of the browser to where the feature was located. I now use a ruler to locate SNPs, simple repeats etc.
57.Wed, 5/2/07 8:55 PMA search function on your site to search the mailing lists. If this is there, I've never found it. I know google will search it, but I haven't been able to figure out how to restrict it to just the mailing lists...
58.Thu, 5/3/07 3:41 PMI don't find the custom track stuff obvious. I will need to look at the on-line tutorials in more detail.
59.Thu, 5/3/07 9:52 PMAbility to load Custom Multiple Sequence Alignments Ability of the Browser, as well as Configure pages, to return to the vertical scroll position when the page was last visited. Right now, every time I click "Show All" for a particular section, or when I return to the Browser after Configuring, the page is refreshed back to the top of the page, and I have to scroll back down to where I was. This disrupts my task. This would be an important improvement.
60.Thu, 5/3/07 10:04 PMI think the UCSC Genome Browser is fantastic. If you're able to handle the new data types, that would be valuable. I like the displays.
61.Fri, 5/4/07 1:32 PMRemove the radiation hybrid marker data from the STS marker track.
62.Fri, 5/4/07 3:23 PMMore ncRNA relevant tracks would be great. Also support for quickly browsing through elements in a custom track would be very useful.
63.Fri, 5/4/07 6:51 PMPlease, set some kind of significance level for the genome aligments to make low matching regions/artifact alignents better visible or exclude these parts from conservation plot.
64.Fri, 5/4/07 6:58 PMIt would be nice to have options to blat larger or more sequences at once (>25); possible in a second priority queue with emial notification reducing the blocking period after submission of 25 sequence batches
65.Fri, 5/4/07 7:56 PMLOH database
66.Fri, 5/4/07 7:56 PMLD tracks!
67.Fri, 5/4/07 8:07 PMamino acid translations in the Get DNA function. Also numbering of the rows.
68.Fri, 5/4/07 9:55 PMMore dynamic display options would be nice. It was great to be able to do track reordering and add and delete custom tracks. Additional options that would be nice would include changing track colors, names, and descriptions.
69.Sat, 5/5/07 12:57 AMOverall I simply think that it is the best damn single internet genomic tool available! Good job! My research is largely dependent upon it anymore and I make sure that all of the new people in the lab are aware of it.
70.Sat, 5/5/07 1:30 AMI would like to have an applet that enables me to blat highlighted sequences in any application, or at least sequences highlighted in a different browser window.
71.Sat, 5/5/07 1:57 AMIt could use a face lift, but there's no better place for genetic and genomic information.
72.Sat, 5/5/07 2:57 AMExpand number of clades and genomes represented.
73.Sat, 5/5/07 10:25 AMChinese language version
74.Sat, 5/5/07 10:35 AMspeed, more speed
75.Sat, 5/5/07 11:37 AMthe possibility to design degenerated sequence for the short match tool (ie : agat(t/g)ga(t/a)c) and to show on the same sequence two, or more, different short matches. Thanks
76.Sat, 5/5/07 1:31 PMMore complete structural variation tracks. An option to have expanded views for only certain coordinates of a track when looking at large regions. Keep a history of viewed regions for quick reference.
77.Sat, 5/5/07 4:23 PMBetter user documentation (more complete descriptions of the custom tracks and more examples) would be a great asset.
78.Sat, 5/5/07 7:02 PMThe blastZ alignments used to make the 17way alignments seems like it could be a lot better. I've recently been looking at the human-chimp-macaque-mouse-rat-dog-cow portions of these alignments. For starters, there are a surprising number of cases where the chimp and macaque sequences are misaligned. A human-chimp sequence will show 10% variation, but that same chimp sequence is 99% identical to the paralogous human sequence. There are also homoplasies where Human = Mouse, Rat, etc, but Macaque and Chimp have a different nucleotide different from the other species. This is because both Macaque and Chimp are aligned to the paraolgous human sequence, not their true ortholog. It looks like the pairwise Net alignments don't have this problem (or least as often). So why aren't the multiple alignments be as good as the pairwise Net alignments? As we begin looking at what's different between species, not just what is conserved, the alignment quality will become more and more important. Your efforts to improve upon the current blastZ style approach will be much appreciated.
79.Sat, 5/5/07 8:18 PMannotation of noncoding RNAs, integration of exisiting small RNA databases
80.Sat, 5/5/07 8:34 PMa guided tutorial? better explanation of lesser used tracks.
81.Sat, 5/5/07 9:31 PMNew ensembl gene links in 2006 gallus gallus assembly browser
82.Sat, 5/5/07 10:26 PM1.Would like to see the conservation graph only for the species that are selected by the user. 2. Would like to see representation of identical bases/amino acids in the page that links to sequence (besides seeing it in the browser window)
83.Sun, 5/6/07 1:41 AMBetter documentation would help. There are many features that one only stumbles over that are very useful.
84.Sun, 5/6/07 3:53 AMno
85.Sun, 5/6/07 11:14 AMa tool to define mitochondrial proteins
86.Sun, 5/6/07 12:32 PMadding plants genomes as well to the genome browser
87.Sun, 5/6/07 1:27 PMinclude data of HapMap as far as possible (blocks, SNPs of population etc.).
88.Sun, 5/6/07 9:45 PMI need more accurate summary when the brouser shows larger genomic region, especially in wiggle track apperance. Otherwise, I need high-resolution output style for larger genomic regions.
89.Mon, 5/7/07 12:27 AMgoogle map, or google earth but for genomic information
90.Mon, 5/7/07 2:11 AMReverse strand display
91.Mon, 5/7/07 5:53 AMIt would be good if the zoom in and out ratios can be revised.
92.Mon, 5/7/07 6:44 AMlink the Zebrafish gene expression database (Zfin) within the UCSC browser. Similarly any gene expression (mRNA insitu/antibody stainings) from other sources to the browser
93.Mon, 5/7/07 8:17 AMmake it easier to export the sequence of genomic regions
94.Mon, 5/7/07 8:25 AMCould you plase map the copy number variants (CNV) on a track, that would be very helpful.
95.Mon, 5/7/07 9:17 AMadd codon numbering: when we look at a codon with a resolution to see the AA translatin it could be nice to see the codon numbering
96.Mon, 5/7/07 11:27 AMTo have a way to copy a subset of what is been displayed, or to choose what to export into another format, like a PDF for instance.
97.Mon, 5/7/07 11:56 AMinclude SNPs from Celera - there is a small subset of SNPs that only occur in www.pantherdb.org
98.Mon, 5/7/07 1:02 PMdesign a visually more "quiet" lay-out if possible
99.Mon, 5/7/07 1:32 PMVery important with a clear distinction between polymorphisms, unknown variants and pathogenic variants. Integration of copynr. variations.
100.Mon, 5/7/07 2:42 PMI annotate the cytochrome P450 genes and I would be interested in an expert track that would be carried forward in new versions. I have tables of data on rat, mouse and human that identify the P450 genes and their locations on your current Browser. I also track the pseudogenes and these would benefit from annotation. Is there any way I can make a contribution to your annotation that will persist beyond the next version? Doing it for each version would be too time consuming. David Nelson dnelson@utmem.edu http://drnelson.utmem.edu/mouse.master.table.html http://drnelson.utmem.edu/rat.master.table.html http://drnelson.utmem.edu/human.P450.table.html mouse is under revision now
101.Mon, 5/7/07 3:37 PMIt would be useful to have a way to directly display the nucleotide position within a specific BAC sequence -- so one could, for example, set the browser to display the sequence between 50kb and 100kb within a particular BAC.
102.Mon, 5/7/07 3:48 PMi'd like to see origins of replications mapped (although i'm not sure how much complete information we have on that). i'd like to see promoters mapped. and promoters linked to the genes that they regulate as well as the transcription factor genes that turn them on. it would be cool too if the expression data could be accessed on a "per tissue" basis. so if i'm interested in breast tissue expression, i could get access to only the genes expressed in the breast.
103.Mon, 5/7/07 5:23 PMIt would be good to have a better way to view SNPs and their proximity to each other, much like you see on the Ensembl site.
104.Mon, 5/7/07 5:31 PMI love your site! One change I would make would be to improve set operations you allow (eg, intersection). In my humble opinion, they don't work correctly. For instance, if you try and grab all the Alus on the human Y chromosome that have no intersection with segmental duplications, some of the hits that return contain said duplications. I know how to 'fix' the problem (by exporting the table for, say, the dupes, and importing again as a custom track), but that solution seems a tad inefficient. Thanks for all of your work! Truly a wonderful site.
105.Mon, 5/7/07 6:14 PMImprove the table browser: when you create custom tracks in the browser from intersections between two other tracks, you often lose information in the results table. For example, if you do the intersection between simple repeats and known genes, you have to use the custom track function to get a list of items, but you lose all of the information except postition and score. I would like to be able to see the information found in the repeat track (ie: size, nucleotide content, sequence, etc) in the custom track output.
106.Mon, 5/7/07 6:26 PMFaster is always better.
107.Mon, 5/7/07 7:12 PMAbility to plot ChIP-chip data as vertical bar graphs overlapping other UCSC genome browser tracts. Thus, each vertical bar represents signal of a single probe from a ChIP-chip experiment. Additionally, some of the more popular ChIP-chip experiments in the literature might be added as standard tracts. Store custom tracks using cookies on users computer so they don't have to be updated every two weeks and this way UCSC server doesn't have to store user custom track data. Expand acceptable custom tract submission to handle format chr:start-stop.
108.Mon, 5/7/07 7:12 PMMore flexible web interface for searching the genome browser table. Ability to enter SQL queries over the web interface.
109.Mon, 5/7/07 8:00 PMOutput data with gene names (list of gene names from interest of regions)
110.Mon, 5/7/07 8:21 PMAllow searching tables using HUGO gene symbols as primary key, resolve discrepancies across reference genes, known genes and HUGO genes.
111.Mon, 5/7/07 8:28 PMI would like to see CNV
112.Mon, 5/7/07 10:06 PMUpdate small RNA population
113.Mon, 5/7/07 10:10 PMKnown Gene List. SNP data.
114.Mon, 5/7/07 10:13 PMadd another zoom tool that would allow you to zoom out to a multiple gene view following a BLAT of a short sequence. A 50X or 100X would be helpful. After searching very short sequences it can take many 10X zoom-out steps to get the view desired. Selecting/typing exact coordinates is tedious.
115.Mon, 5/7/07 10:34 PMMore up to date miRNA target tracks; especially experimentally verified targets
116.Mon, 5/7/07 10:36 PMMake it easier to customize which tracks are showing. The "full,dense" options are confusing. I think checkboxes would be better than pull-down menus. It's hard to find particular tracks in the long list of pulll-down menus. Have extra information (from clicking on something in the window) appear in another window.
117.Mon, 5/7/07 11:06 PMSequence retrieval should be expanded to mRNA sequences i.e. Equivalent of the DNA option: would allow you to obtain the sequence of an mRNA in the current window
118.Mon, 5/7/07 11:11 PMI'd love a clearer explanation, linked from the export page, of what the numbers represent when one tries to download ChIP/chip data. Thanks -- I tell all my friends about your genome browser. I'm only half kidding.
119.Mon, 5/7/07 11:29 PM I would like more flexibility for user tracks, we find that .wig format gives the best display for quantitative data, but doesn't support overlapping coordinates. We produce a file optimized for display and it gets used as a data source. The amplicon coordinates aren't precise because of compromises made to produce the display. This has caused confusion. The .wig format using the span format results in the data point off center with respect to the display when someone uses the file for data analysis. The general issue of using the UCSC site as a data repository might be worth examining. It is fantastic to have a single site from which lots of data can be obtained. The ability to store more information with each data point could be useful for the repository function.
120.Tue, 5/8/07 1:27 AMIs it possible to create links from the genome browser to other search engines (e.g., Ensembl)? This would be a great resource for helping to map (in silico) the relative positions of genes using multiple search engines.
121.Tue, 5/8/07 2:29 AMBetter doucumentation on the FTP site downloads for text and MySQL tables. The annotation is "try to guess" level.
122.Tue, 5/8/07 7:15 AMUpstream regions or transcriptional starting sites of known genes Known gene prediction of mouse, rat,... as well as human
123.Tue, 5/8/07 9:45 AMImprove the human pseudogene retrieval methods.
124.Tue, 5/8/07 12:45 PMidentify NCI-60 cell lines unambiguously
125.Tue, 5/8/07 1:52 PMyou may extend the description of the tracks
126.Tue, 5/8/07 3:13 PMI love it as it is- though I am sure you will get a lot of worthy comments!
127.Tue, 5/8/07 3:15 PMBecause of multiple isoforms and entries in RefSeq and UCSC for a single gene, I often find it hard to figure out which one to click in order to get the maximum amount of information about the gene's structure and function. The redundancy of these entries doesn't seem to be incorporated well into a single, coherent page about the gene function, exon structure, alternate isoforms, etc.
128.Tue, 5/8/07 3:54 PMAPI support!
129.Tue, 5/8/07 4:11 PM1. Split the STS track so that polymorphic markers, currently identified in blue, are in a separate track. When the window is covering a large region, there are so many non-polymorphic STSs that the track is automatically collapsed, making it difficult to identify genetic markers. The identification of polymorphic STSs in the track is somewhat imperfect, but this would still be helpful for designing genetic fine mapping protocols. 2. It would be VERY helpful to have a scrolling window. The right-left arrow buttons are difficult to use because the size of the jump seems dependent on the window size, which is freely variable. So it`s hard to do some things like walk from exon to exon in a gene with very large introns. The 3x zoom button is helpful, but it does not work in all browser windows.
130.Tue, 5/8/07 4:30 PMBETTER TRANCRIPTION FACTOR BINDING SITE TRACKS, MORE OPTIONS, NOT ONLY FOR HUMAN
131.Tue, 5/8/07 5:40 PM1:By the getting of DNA-Sequenc you dont offer the sequenc with their numbers for example: 50 aacc............... 100 ttgcc.............. 150 taagc..... 2:It is very difficult to find the promotor and Exons parts from genes I love your site:))god bles you javadkarimzad@yahoo.de
132.Tue, 5/8/07 5:53 PMSome minor usability things - chromosome position input boxes should be a little more tolerant about input delimiters, e.g. allow spaces instead of requiring chr:start-stop.
133.Tue, 5/8/07 6:04 PMImprove reliability of display of requested information. For example, I use the Genome Graphs to display chr infor. However, when I click on a chromosome, it shows a small segment of the chromosome. When I click to zoom out to see more of the chromosome, it often times only shows the idiogram, and is then "done" (ask indicated at the lower left corner) with the page display. Reloading does not help.
134.Tue, 5/8/07 6:23 PMnone
135.Tue, 5/8/07 6:51 PMThanks for a wonderful tool.
136.Tue, 5/8/07 7:39 PMThe conservation fast cons tracks are very important I would like to see more species added.
137.Wed, 5/9/07 1:29 AMadd prediction set of transcription factors binding sites
138.Wed, 5/9/07 6:43 AMEasier tools for visualizing microarray data on the genome browser.
139.Wed, 5/9/07 6:59 AMIncluding a database of known transcription start sites (5'UTR) and start of the coding region and label functional known Promotor elements, both with link to the relevant reference. It would be fine to be able to choose known Protein binding sites.
140.Wed, 5/9/07 10:47 AMmake it easier to get from the browser to the underlying sequences - particularly for genomes that are not well annotated.
141.Wed, 5/9/07 12:58 PMNot such a fundamental problem, but I find confusing the "fake" result that is showed whenever a genome location could not be found. I guess that's something that could quite easily be fixed.
142.Wed, 5/9/07 1:38 PMreintroduce toools to design primers for ampification of multiple exons promoters starting from genomic sequence (eg primer3)
143.Wed, 5/9/07 4:26 PMImprove decorated FASTA output. Would be good if certain features (e.g. dbSNP rs numbers) could be included in the output. Something like the SeattleSNPs colorFasta format. I appreciate this could be very difficult to implement!
144.Wed, 5/9/07 6:44 PMI would like that to find SNPs could be more easy!
145.Wed, 5/9/07 7:33 PMMore customizable tracks
146.Wed, 5/9/07 8:09 PMtransciption factor binding analysis in conserved elements
147.Wed, 5/9/07 9:29 PMMake exporting sequences such as promoter sequences for one particular gene or whole genome genes an easy task.
148.Wed, 5/9/07 11:00 PMadd links to Human Genome Segmental Duplication Database and to view the CNV's directly on the UCSC browser
149.Thu, 5/10/07 12:18 AMMaybe other way of seeing data... massive amount of data...2D is good only if you want a specific question... if you have a broader question and you want to see the structure of the genome, it is difficult to do it with the available visualisation. Move window by click and drag.
150.Thu, 5/10/07 7:23 AMmore fish genomes on the conservation track. the conservation track is useful (if there is enough conservation) in designing transgenes, etc., since it gives a guide where the promotor and other features probably are.
151.Thu, 5/10/07 8:04 AMInstead of the arrows above the broswer window to navigate along a chromosome, provide a function that allows one to centre the window on a given gene or feature (akin to Ensembl browser).
152.Thu, 5/10/07 1:29 PMplease update the rat genome, it's soon 3 years old.
153.Thu, 5/10/07 1:52 PMA smooth zoom out and zoom in feature would help immensely (similar to affymetrix IGB)
154.Thu, 5/10/07 4:01 PM1) Display LD/haplotype blocks in 2006 version. 2) Not clear how Allen brain data is displayed in browser 3) Have 2 options in SNP display: retain the way it is shown currently and have the option of displaying only those SNPs supported by real data or have data on heterozygosity 4) Indicate miRNA locations 5) Develop an alignment tool for short peptides or full-length proteins akin to BLAT. 6) Indicate predicted motifs in proteins
155.Thu, 5/10/07 4:03 PMtraining on line, or phone availability or quick animated demos
156.Thu, 5/10/07 6:23 PMAn easier way to add my own data (including exons that are not annotated) to the browser. It's not intuitive.
157.Thu, 5/10/07 8:14 PMEasier to download images in ways that can be edited in a program such as Adobe Illustrator. Currently, must download PDFs which often are exceptionally hard to edit (all kinds of postscript obejcts that mask the key elements). Another way of phrasing this request would be to ask for a FAQ with examples of how to take a UCSC browser dispaly and turn it into various images suitable for PowerPoint.
158.Thu, 5/10/07 9:23 PMAs-is the browser prints poorly with IE, forcing one to create PDFs or screenshots in order to make a hardcopy. Easier printing would be better.
159.Fri, 5/11/07 4:41 AMIt would be nice to resolve the issue where the same SNP got 3 rsNumbers. Something like the Convert tool would be nice to SNP conversions.
160.Fri, 5/11/07 10:37 AM-
161.Fri, 5/11/07 10:37 AMOf course, you can always improve something. But I think UCSC Genome Browser is one ...no.. the best molecular biology site in the net.
162.Fri, 5/11/07 11:05 AMCurrently, after searching for a gene (e.g. MAPK), a long list of genes comes up. If you click on the gene you want, a new screen shows you the genes chromosomal position. If you click on your gene in the picture, you get information about the gene. This is a very poor, inefficient userface. I would like the list of genes to come up at the side of the screen, and then have the chromosomal position shown in the centre of the screen. That way I'd be able to click on each of the different MAPKs to see their positions etc WITHOUT having to forever press the back button. In addition, it would be useful to have a link that goes straight from the gene list to the information page, without having to go via the map. If my thoughts are not clear, feel free to email me at neil.goddard@icr.ac.uk for more details.
163.Fri, 5/11/07 1:41 PMI would like to be able to see all the custom tracks that are available.
164.Fri, 5/11/07 4:41 PMan API that i can use to grab information in a more interactive manner. (the table browser is good, but i want more.) i want to be able to make use of the browser data you return, which right now is an image- useless for me to add value to it. i have no idea where i that display there is, say, an exon i want to hilight or do something with. you should provide a real data stream back for the current view- one that is interpretable on my end. you should have a my-end client that interprets that stream and makes the image on my machine. that way i can add value to the image as it is built on my end. there are many more, but i know you don't have the time :)
165.Fri, 5/11/07 5:15 PMGreat site already!
166.Fri, 5/11/07 8:20 PMIt would be nice to post an announcement when you remove tracks with an explanation as to why, such as recently happened with the 5 species regulatory conservation track.
167.Sat, 5/12/07 9:11 AMTable browser should be able to take in several custom tracks and determine where all the tracks intersect with known genes and then export a list of genes AND gene positions not just genes.
168.Sat, 5/12/07 3:36 PMneed better control of table outputs.. the intersection stuff is too complicated and frequently does not give a reasonable output.. we need a preview function and specific drill downs that let you say what will be in each column.. dont know if it can be done effectively with html, but ensmart certainly does a better job
169.Sat, 5/12/07 9:08 PMfunctional RNAs to include tRNAs, rRNAs
170.Sun, 5/13/07 1:08 PMThere are some tracks on the Ensembl browser that are not on the UCSC browser, such as DECIPHER, and MICER, etc that should be added so that the sites are equivalent. Ensembl is terrible and it would be nice to see things in UCSC. It would be nice to have access to the older versions of the browser.
171.Sun, 5/13/07 7:33 PMCongratulations on the continuing excellence of your site, which I always show to students first. It is generally highly comprehensible. ENSEMBL, though excellent in content has the visual appeal and comprehensibility of a train timetable. There are some things that your browser doesn't seem to do. Some genomes that you carry were, when I last checked, unavailable at NCBI or ENSEMBL. That's obviously a plus for you and some of those genomes are very interesting in looking at evolution of mammalian genes. Neither you nor ENSEMBL(I think) have a PSI_BLAST server, which I have found very useful for finding gene family members that other algorithms (apart from threaders) do not appear to fin...BLAT, though fantastically useful much of the time is far too insensitive for this. The form needs to have the facility to paste in a PSSM.
172.Sun, 5/13/07 10:00 PMKeep server response FAST, keep interface simple. Advanced features should all have a "help" link to basic information for those with minimal knowledge of mol bio and genetics.
173.Mon, 5/14/07 4:46 AMHave more fully functional mirror sites. Now the mirros I tried do not have many functions including Blat.
174.Mon, 5/14/07 10:21 AMCustom tracks, I think, were your best wonderful ideas!! I enjoy using them every day looking at my data. By the way, it'd be very useful if managing custom tracks could be possible to move up and down tracks therefore changing their relative position simply clicking a button or an arrow instead to write this information in the track line; infact when you have a lot of tracks and you want to insert a new one among other two in the middle position, you have to re-number all the others accordantly. Thanx a lot for all your work!!!
175.Mon, 5/14/07 1:07 PMMore flexibility when displaying custom tracks / own data (e.g. possibility to display lines or average over regions)
176.Mon, 5/14/07 1:08 PMI would like to see mouse inbred strains genomic data incorporated into the bowser.
177.Mon, 5/14/07 1:49 PMWhen blat or blast is used to find a matching sequence you got the answer in position on a specific chromosome. If the matching sequence is within a gene it would be helpful to get information about the position within the gene as well, i.e. which exon. Also when you browse for a sequence, you see the exones as blocks but it would be very helpful if you also could se which exon each block is representing.
178.Mon, 5/14/07 3:42 PMtranscription factor biding site
179.Mon, 5/14/07 5:38 PMmore flexibility with custom tracks
180.Mon, 5/14/07 6:20 PMWhen exporting data, allow to use colors and to combine them with Upper and Lower case sequences. Mapping Protein Domains to the Genes are EXTREMLY important. I use the Ensemble facility just for this and their SNP and amino acid alignments on the genes, otherwise I love the UCSC site.
181.Mon, 5/14/07 8:08 PMSee multiple alignements of many species (i.e. mammals) in all mammal browsers, not just in human browser.
182.Mon, 5/14/07 10:44 PMno idea
183.Mon, 5/14/07 11:23 PMSome tracks contain high-resolution information, while some are for low-resolution ones. It is awkward to display high-resolution info over a large-scale window, and vice versa. E.g, it is pointless to show some thousand genes in a region with >20M bp.
184.Tue, 5/15/07 1:56 AMAddition of HapMap LD tracks to Human Mar 2006 assembly Links to Jackson Labs phenotype data for mouse genes
185.Tue, 5/15/07 2:29 AMI WANT TO WORK IN CHINESE,AND BEST WISHES TO YOUR STAFF
186.Tue, 5/15/07 10:33 AMIn generatl I think that the browser is a great tool and me and others in my lab use it a lot (both via the browser and directly on our local downloaded sql data) One of the major difficulties we face is the conversion between the various acessions. here are many ocasions in which you can enter an accession to the browser and get "your gene" while trying to do that automatically is not always clear. And we usually need to do some very strange queries on the data to get what we need. A friendly converter might help (and files that convert to/from refseq in addition to those that convert to/from knowngene)
187.Tue, 5/15/07 10:45 AM1) Swap strands feature. 2) Zooming window.
188.Tue, 5/15/07 1:37 PMin the viewer itself: you can choose to view a lot of stuff; maybe a link to a new page with all the additional stuff you can make 'full' etc. etc. cleans up the viewer window nicely
189.Tue, 5/15/07 1:46 PMspeed is the main problem, the dataset are excellent and the updates listed above would undoubtedly increase utility - as long as the speed improves!
190.Tue, 5/15/07 1:54 PMMake improvements in the process for adding custom tracks, possibly by writing a tool that takes care of the exact formatting necessary to ensure a smooth upload. Preferably non-web browser based.
191.Tue, 5/15/07 3:26 PMmore beautiful
192.Tue, 5/15/07 3:55 PMI like the ability to cut and paste annotated sequence data (e.g. gene exon and flanking intron sequence as in ENSEMBL) into project folders for gene mutation hunting. The current 'DNA' options are good but perhaps not very flexible.
193.Tue, 5/15/07 4:48 PMan even better table browser. and i find the documentation and "how to use" instructions for the table browser a little telepgraphic.
194.Tue, 5/15/07 10:51 PMThe possibility to search a specified chromosome during BLAT searching
195.Wed, 5/16/07 2:03 AMIt is difficult to navigate at times - I would like to be able to click on a gene in the browser to zoom in on it, and I can't work out how to get out the sequence for the region displayed. I think it should be simple, but there's not an obvious (to me) option for doing so.
196.Wed, 5/16/07 4:27 AMPlease include Affymetrix infomation, as the Ensambl genome browser do. It will be very valuable. This is the only reason I am still using Ensembl genome browser at all. Thank you.
197.Wed, 5/16/07 8:14 AMuse strict xhtml for your pages save graphics as SVG make an update to your DAS server to produce something than would be more readable for a human. put the src on a CVS repository so anybody can propose some improvement to the code.
198.Wed, 5/16/07 11:53 AMnone
199.Thu, 5/17/07 1:49 PMi find it hard to move left and right and get to where i want to go without using numbers. some sort of visual method such as highlighting the area i want displayed.
200.Thu, 5/17/07 4:57 PMTHe whole set of Structural variation complete as the published in different human genome co-ordinate
201.Thu, 5/17/07 5:04 PMGiven CSHL meeting, perhaps some suggestion of binding energies in promotor regions of known genes?
202.Thu, 5/17/07 5:24 PMWeb services or a programming api with functions to retrieve information in a high-throughput manner.
203.Thu, 5/17/07 6:59 PMnone
204.Thu, 5/17/07 8:49 PMClean up of inconsistencies, for instance in the gene annotations
205.Fri, 5/18/07 3:56 AMi often design primers using the HG data on GB and then do in silco PCR with GB and return no results. This just doesnt make sense -- they use the same sequence??!?!
206.Fri, 5/18/07 4:58 AMSome siganl pathway information
207.Fri, 5/18/07 4:26 PMmap the dog 2 million SNP set on both canfam1 and canfam2 assebly
208.Fri, 5/18/07 7:10 PMWhen I look for a sequence on the UCSC site, I used to find the "sequence view" variations easily. That has been hard lately. I like having the variant nucleotides displayed right under the sequence -- it is good to see for us in molecular diagnostics, as the SNP DB is a pain to use. I don't think it is necessary to have multiple lines indicating the mRNAs under the sequence -- they just take up space. The initial display of a sequence diagram with the alternative splice forms is useful, even though some of these are aberrant, since one sees them in one's work.
209.Sat, 5/19/07 1:18 AM1) Revision Control! I'd like to see the browser and related tracks with version numbers. I have very difficult time to get REPRODUCIBLE results when using your site because the data changes out from under me all the time. I try to keep some local data on my machine but it seems impossible to predict everything I might need. 2) Explanations of the various tables in the Table Browser. It can be very difficult to do things like find orthologs between species, even though you have the data for it, because it is unclear which entries of which tables to use. 3) ...It would be nice to have more species in the proteome browser.
210.Sat, 5/19/07 1:57 AMImprove ability to download alignments of query sequence and other homologous sequences
211.Sun, 5/20/07 10:27 AMBrowse two or more loci, associated through chains or nets, in the same window, with the aligned regions highlighted. Ensembl has a mode for this, but it does not work well.
212.Sun, 5/20/07 5:07 PM1- Please help us to find clones already sequenced. Usually you change the BAC name to Acession name and we can't find the BAC/PAC/Fosmid anymore. NCBI page is better under that point of view. 2- Expand the BLAt size limit
213.Sun, 5/20/07 7:51 PMPlease map dog 2M SNP to both canfam1 and canfam2
214.Mon, 5/21/07 5:45 AMok
215.Mon, 5/21/07 8:29 AM I'd suggest to consider all improvements very carefully and just in case to launch side projects, because currently I believe the browser covers the great deal of the needs of the audience, at least at the pilot genome scan for the targets. I always check for the isoforms over here.
216.Mon, 5/21/07 2:52 PMPlease include dog SNPs for CanFam2 instead of just CanFam1
217.Mon, 5/21/07 7:05 PMA minor suggestion. If it is possible to make available full text/pdfs or LaTex files for the references that support/explain the data tracks, I think it would be convenient and useful for users. It might also increase UCSC related citations. Of course this might require navigating copyright issues, but if a user gets a notice regarding academic use maybe that would be enough?
218.Mon, 5/21/07 9:15 PMSet up personalized display of tracks.
219.Tue, 5/22/07 7:36 AMavailabality through Taverna
220.Tue, 5/22/07 12:16 PMIs it possible to organize courses to help researchers to become familiar with the UCSC Genome Browser ? Including in Europe ? For instance, we recently invited a person from ENSEMBL for a full day presentation - that was really useful
221.Tue, 5/22/07 12:33 PMIt would be good with complete inter-genome lifOver-chains among all vertebrates. As it is now it varies from version to version which genomes are included.
222.Tue, 5/22/07 5:25 PMI would appreciate if you can add Neurospora crassa genome data in.
223.Tue, 5/22/07 6:26 PMimprovements of the additional material for zebrafish alignments and conservation with other vertebrate genomes
224.Tue, 5/22/07 8:13 PMRNA protein interactions
225.Wed, 5/23/07 11:16 AMAccess to Multiple alignment files for mammals genome only
226.Wed, 5/23/07 2:18 PMI'd like to see more flexibility in the Table Browser for producing custom datasets
227.Wed, 5/23/07 5:05 PMmethylation signature of analyzed regions
228.Wed, 5/23/07 11:07 PMThis is a great set of tools! When looking at the sequence alignments for multiple species, it would be nice to have some sort of graphic showing where the selected "blocks" of conservation are within the selected range. Right now it's hard to tell which areas of the sequence are being displayed without having several windows open.
229.Thu, 5/24/07 8:50 AMmake available sequence of gene with mRNA sequence exon and introns marked on sequence. Make possible to retreive specified DNA sequences from positions given
230.Thu, 5/24/07 1:14 PMSome way of drawing abox around a region of interest to zoom in quickly
231.Thu, 5/24/07 3:18 PM1) SNP names should reference location in a reference genome, the RS system is counter-productive 2) 100 bp flanks should accompany a SNP record in addition to 1) 3) Each (known) gene should have an associated file including 50000 bp (e.g. -50000 to -1) of the 3' and 5' regions that can be download with a click. Note, in 1) and 2), SNP can be any segment or mutation of interest.
232.Thu, 5/24/07 7:51 PMThe main problem is the incredibly non-intuitive nature of the site. It is the antithesis of user-friendly. Take a look at the ensembl site and you will see how cumbersome this site is
233.Fri, 5/25/07 12:33 AMLinks to Ensembl
234.Fri, 5/25/07 6:50 AMIt would be really, really awesome if the genes for the sea urchin genome (purpuratus) were aligned to the sea urchin genome, although the non-purpuratus genes were very nice.
235.Fri, 5/25/07 10:17 AMWhen you get gene name wrong, or if it can not find the appropriate hit, i find it very annoying that it takes you to a random location in the genome. I would prefer it to just say no hit was found - and leave your search item in the white box so that it can be corrected. Also, after you search for something and click on your hit, I think there should then be two white boxes on the genome browser site. One which keeps the chromosome position as normal and allows you to change it, and the other that retains your original search item. Within the genome browser, I'd like to see those faint vertical blue bars separated to an appropriate scale, so that it is easy to count distances in the genome. I recommended this before and thought it was going to happen but it appears not to.
236.Fri, 5/25/07 9:35 PMAdditional features for the gene graphs. For example, the ability to change marker size.
237.Sun, 5/27/07 7:22 AMAJAX support for the browser, better documented web services API, better support for integrating third party annotations (cf. BioDAS in Ensembl), UCSC scripting support for Perl, Python, Ruby (cf. Ensembl api)
238.Sun, 5/27/07 1:30 PMeasier navigation or help pages, examples of how to find things
239.Tue, 5/29/07 4:26 AMThis may already be covered by a FAQ - but often some feature appears in the UCSC Browser that is very useful but then it disappears some time later. It would be good to be able to choose from the complete functionalities that have been developed - or is this too cumbersome?
240.Tue, 5/29/07 6:39 PM1. Allow multiple user-defined tracks to be loaded at once. 2. Allow longer user track names on the left (currently they can get cut off). 3. Slider to allow more control over the view (rather than just 1.5x, 3x, 10x and >, >>, >>>). 4. Allow settings to be easily saved so that it is easier to switch between two types of settings (i.e. display Settings A which shows a lot of tracks for everyday use, then quickly switch to Settings B which shows just the essentials for use in making figures for presentations.
241.Tue, 5/29/07 8:47 PMMore invertebrate genomes... Apis? Tribolium? With the same user-friendly interface that those genomes don't have.. the UCSC brower is AWESOME. Thank you so much!
242.Wed, 5/30/07 8:25 AMThe splicing info has improved a lot but some colour coding of different regions of transcripts would help immensely in identifying them. We have used a system where we compare to the oldest refseq and colour coded changes in introns and exons based on the splice sites used (GT-AG = dark green for introns and exons same as refseq; light green for changed exons. GC-AG used blue, light blue and AT-AC used red, light red). Changes which occur at non-canonical splice junctions could appear as grey. Then you can easily see changes and see whether they occur at bone fide splice junctions.
243.Wed, 5/30/07 11:25 AMIf and when polymorphisms are included, site source/ reference
244.Wed, 5/30/07 11:03 PMInclude exon number designations, and have the ability to know the codon number in a protein with a nonsynonymous snp (Genewindow from the NCI CGAP/CGF site does this well, but they do not have a BLAT like function - I often have the two browsers open)
245.Thu, 5/31/07 1:32 PMIt'd be cool if you could have a log in where it permanently remembers what settings you like for each species and your custom tracks.
246.Thu, 5/31/07 8:43 PMAdd Arabidopsis for DNA methylation studies