Profile hidden Markov models for biological sequence analysis.

Software for the exploration of lightweight stochastic context free grammars

This is the code accompanying Robin Dowell's paper "Evaluation of Several Lightweight Stochastic Context-Free Grammars for RNA Secondary Structure Prediction", BMC Bioinformatics 5:71, 2004. It implements several small SCFGs for single-sequence RNA secondary structure prediction.

Sequence database searching with RNA structure queries.

RSEARCH aligns an RNA query to target sequences, using SCFG algorithms to score both secondary structure and primary sequence alignment simultaneously. It's slow, but somewhat more capable of finding significant remote RNA structure homologies than sequence alignment methods like BLAST. (By slow, we mean, you really need a substantial computing cluster to do any serious work with it; a typical single search of a metazoan genome may take a few thousand CPU hours).

tRNA detection in large-scale genome sequence.

tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second. It was implemented for large-scale human genome sequence analysis, but is applicable to other DNAs as well. It applies our COVE software (see below) with a carefully built tRNA covariance model, while getting around COVE's speed limitations by using two tRNA finding programs from other research groups as fast first-pass scanners (Fichant and Burks', and an implementation of an algorithm from A. Pavesi's group). It runs on any UNIX system with Perl and a C compiler installed.

Inference of orthology and paralogy relationships in gene trees.

Fast Pattern searching for RNA secondary structures.

RNABOB is an implementation of D. Gautheret's RNAMOT, but with a different underlying algorithm using a nondeterministic finite state machine with node rewriting rules. (Computer scientists would probably cringe in horror. It works, and it's fast, but is it street legal in a computer science department? Who knows.) An RNABOB motif is a consensus pattern a la PROSITE patterns, but with base-pairing.

A C library that much of the above software bundles in.
C function library for sequence analysis.

SQUID is my own personal library of C functions and utility programs for sequence analysis. I don't really suggest that you use it in your programs, as I change it at will. However, it does contains some small utility programs that some people have found useful in scripts that drive large HMMER tasks.

Robin Dowell's prototype of a Perl/Tk application for viewing profile HMMs created by HMMER, including the Pfam database.