HMMER The HMMER hidden Markov model software package and other software for large-scale genome analysis using probabilistic models of proteins and RNAs, from Sean Eddy's lab at Washington University, St. Louis USA. HMMER -- Hidden Markov models for sequence profile analysis. Hidden Markov model based profiles (profile-HMMs) can be used to do sensitive database searching and multiple sequence alignment, using statistical descriptions of a sequence family's consensus. PFAM -- a database of multiple alignments covering most well known protein domain families, including things like SH2, kinase catalytic domains, immunoglobulin superfamily domains, and so on. COVE -- an implementation of stochastic context free grammar methods for RNA sequence/structure analysis. TRNASCAN-SE -- tRNA detection in large-scale genome sequence. RNABOB -- Pattern searching for RNA secondary structures. SQUID -- A C library that much of the above software bundles in.

Current Version:   N/A License Type:   GNU GPL

Home Site: http://genome.wustl.edu/eddy/hmm.html Source Code Availability:   Yes Available Binary Packages: Debian Package:   No RedHat RPM Package:   No Other Packages:   yes (tar.Z) Targeted Platforms: SGI, Intel/Linux, Sun, DEC Alpha, MasPar. Software/Hardware Requirements: ANSI C Compiler.

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