• Software
• Databases
• Other Computational Biology Homepages
• Biology Search Sites
• Educational Resources for Biology

This web page prepared by Richard Fiorito, for a class in Computational Biology, taught by Peter Clote at Boston College in Spring 1998.

Sites that offer software applicable to the material that will be covered in MC699

• RNAdraw Homepage --A Windows95 application for RNA secondary structure prediction
• Mfold Ftp Directory --Zucker's mfold application for UNIX workstations
• RNAstructure Homepage --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 UNIX workstations
• HMMER --Hidden Markov Model Software produced by the Eddy Lab at Washington University
• SAM --Sequence alignment modelling system software from the University of California, Santa Cruz
• WPDB --The protein databank through Windows (comes with RasWin, which is the Windows version of RasMol)
• Swiss-Pdb Viewer --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

    PFAM	Search a protein sequence against the PFAM HMM database of common protein domains.
    tRNAscan-SE	Find and annotate tRNA genes in a DNA sequence

  • Software

    HMMER	Hidden Markov models for sequence profile analysis.
    PFAM	The PFAM (protein families) HMM database and Web server.
    COVE	RNA structure analysis using covariance models.
    TRNASCAN-SE	tRNA detection in genome sequences.
    RNABOB	Pattern searching for RNA secondary structures.
    PKNOTS	A dynamic programming algorithm for optimal RNA folding, while including RNA pseudoknots.
    SQUID	A C library that much of the above software bundles in.

Sites that offer databases for use with some of the software packages listed above

• Guide RNA Database
• Nucleosome DNA sequences
• Brookhaven National Laboratories Protein Databank --Site to download and search for *.pdb files
• Genomic Databases --Genome databases of various species from BioBase
• snoRNAdb, database of small nucleolar RNA genes found in yeast, from Eddy's Lab at Washington University, St. Louis.

Some important Computational Biology Homepages

• University of California, Santa Cruz
• The University of Vienna's Theoretical Biochemistry Group
• The Turner Group
• The Genome Sequencing Center --Located at Washington University in St. Louis
• SDSC --A national laboratory for Computational Science and Engineering
• Sanger Center, Cambridge, England
• Genome Sequencing Center home page , Washington University.
• RNA World at IMB Jena, Germany.

Molecular Biology Search Sites

• National Center for Biological Information --This site includes BLAST, PubMed, Entrez, BankIt, OMIM, Taxonomy, Structure, and many others. The site is full of other resources as well

Some Sites that Offer Information on Molecular Biology and Other Aspects of Biology

• Zuker's RNA Resource Page
• RNA Information Page
• An Educational Resource Page for Biochemistry and Molecular Biology
• An Educational Resource Page for Cladistics and Taxonomy