CPBS 7711 links

General computational biology sites

• UCHSC's Center for Computational Pharmacology and Bioinformatics Ph.D. program information
• International Society for Computational Biology

• Journals

  • PLoS Computational Biology
  • Bioinformatics (journal)
  • Journal of Computational Biology
  • Journal of Biomedical Informatics
  • BMC Bioinformatics
  • Statistical Applications in Genetics and Molecular Biology

• Conferences

  • Pacific Symposium on Biocomputing Conference site with free full text proceedings.
  • Intelligent Systems for Molecular Biology (ISMB) with free online conference proceedings. Also, the announcement for the 2010 conference
  • RECOMB 2010 conference
  • Rocky Mountain Regional Bioinformatics Meeting

Lecture-related web sites

Course Project

• NIH's application forms and instructions
• NIH's general review criteria for all grants.
• NIH's information page for peer reviewers. Especially Reviewer Orientation and Overall Impact vs. Significance There are also a set of FAQs and case studies / examples
• Look at the Journals and Conferences listed above for successful other projects (perhaps larger in scope than your course project).
• Summer rotation projects from Comp Bio Students
• Advice or suggestions about grad student research projects from other bioinformatics programs: Manchester Google summer of code UCSD UCSC

Database Search and Sequence Alignment

• Various lecture notes on Dynamic Programming, from: GWU's computer science class
• A basic Java Applet demonstrating various sequence alignment algorithms
• BLAST
• code for computing PAM (Point-Accepted Mutations) using Dayhoff matrices

Multiple Sequence Alignments

Remember, none of these are optimal, so looking at the various different alignments they produce can be useful.

• ClustalW2 progressive MSA program
• DCA Divide and Conquer MSA
• DALIGN block based MSA
• Tmsa, IBM's pattern based MSA
• FSA (source code), a method for multiple alignment of large genomic sequences.
• STRAP, a structurally-oriented MSA site.
• A somewhat dated but still useful gentle guide to multiple alignment with self-assessment questions and links

Hidden Markov Models

• SAM, an HMM creation tool, with documentation, a web server, and a download page. NB: you must fill out and return a free (as in beer) academic license form to download it.
• HMMer, a similar HMM creation tool, with documentation and free (as in GPL) downloading
• Pfam A protein family database built with HMMs.

Molecular Biology Databases

• NAR annual compilation of Molecular Biology Databases
• National Center for Biotechnology Information (NCBI) and specific NCBI sites:
  • Site Map & Educational resources especially the tutorials
  • Entrez (search everything) and Entrez Gene (curated compilations by gene)
  • BLAST (sequence-based searches)
  • PubMed (the biomedical literature, with links to holdings in the UCHSC library)
• UniProt (curated protein information, includes SwissProt and TrEMBL).
• PDB (protein structures)
• InterPro (protein families and motifs)
• The Gene Ontology (molecular biology conceptual structure, with mappings to particular genes), see also OBO
• Santa Cruz "Golden Path" (configurable human genome browser)
• DIP (database of interacting proteins) and MINT, a competitor.
• Kyoto Encylopedia of Genes and Genomes (KEGG) (metabolic and signalling pathways)
• Enzyme DB (US mirror) (enzyme activities), and Reactome, a human-specific competitor. Also consider MetaCyc
• The Human Genome Nomenclature Committee (HGNC) for gene names.
• The Human Protein Reference Database (HPRD)
• Regulatory information databases, such as Transfac, COMPEL, Jaspar, and Mapper, EPD and CREB
• Information Hyperlinked over Proteins (IHOP) generated by text mining.