SAL Home OTHERS Chemistry, Biology & Related


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:

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.

Other Links:

Mailing Lists/USENET News Groups:


User Comments:

  • None

See A Screen Shot? (Not Yet)

  SAL Home   |   Other Scientific Fields   |   Chemistry, Biology & Related

Comments? SAL@KachinaTech.COM
Copyright © 1995-2001 by Herng-Jeng Jou
Copyright © 1997-2001 by Kachina Technologies, Inc.
All rights reserved.