Computational Biology Resources
This web page prepared by Richard Fiorito, for a
class in Computational Biology, taught by Peter Clote
at Boston College in Spring 1998.
--A Windows95 application for RNA secondary structure prediction
Mfold Ftp Directory
--Zucker's mfold application for UNIX workstations
--A C++ code version of Zucker's mfold application for Windows95
Vienna RNA Package
--The University of Vienna's RNA secondary structure prediction and comparison software for
--Hidden Markov Model Software produced by the Eddy Lab at Washington University
--Sequence alignment modelling system software from the University of California, Santa Cruz
--The protein databank through Windows (comes with RasWin, which is the Windows version of
--Software from the Geneva Biomedical Research Institute similar to RasMol
that will work on a Macintosh
The following software links are to the group of Sean Eddy
at the Washington University in St. Louis.
- Biosequence analysis compute servers
|| Search a protein sequence against the PFAM HMM database of
common protein domains.
|| Find and annotate tRNA genes in a DNA sequence
|| Hidden Markov models for sequence profile analysis.
|| The PFAM (protein families) HMM database and Web server.
|| RNA structure analysis using covariance models.
|| tRNA detection in genome sequences.
|| Pattern searching for RNA secondary structures.
|| A dynamic programming algorithm for optimal RNA folding,
while including RNA pseudoknots.
|| A C library that much of the above software bundles in.