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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
- 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
- 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
Source Code Availability: Yes
Available Binary Packages:
- Debian Package: No
- RedHat RPM Package: No
- Other Packages: yes (tar.Z)
SGI, Intel/Linux, Sun, DEC Alpha, MasPar.
ANSI C Compiler.
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