CBSE Bioinformatics Documentation

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Bioinformatics & Computational Biology at UCSC

SAM Sequence Alignment and Modeling Software System documentation

Dirichlet mixtures Used in various projects for modeling the prior expectation of the distribution of amino acids.

A2M multiple-alignment format Used in most of the SAM tools for multiple alignments—one of the few formats that can express unaligned positions.

CVS Version Control How to use our local version of CVS.

RDB Simple, flat-file relational databases. Download the RDB 2.6c source: This copy is patched to correctly handle sorting numbers in exponential form. Requires PERL5 and GNU sort (gsort).

SVM.1.0 Support vector machine software

DBGET Unix commands for accessing the bioinfomatics database at GenomeNet

Gnuplot Version 3.6 beta Installed as the command gnuplot3.6. Warning: this page is large.

DOC++ A Documentation System for C/C++ and Java. Used JavaDoc-like syntax.

dssp-get Get the path to a DSSP file, downloading if necessary.

hssp-get Get the path to a HSSP file, downloading if necessary.

pdb-get Get the path to a PDB file, downloading if necessary.

PDB Info Files Abbreviated PDB file and ATOM/SEQRES alignment in RDB format.

pdb-get-info Get the path to a PDB info file, create if necessary.

UCSC Internal Documentation Directory



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© January 2005, CBSE Updated 5/2008