Bioi 7711 links
General bioinformatics sites
- UCHSC's Center for Computational Pharmacology and Bioinformatics Ph.D. program information
- International Society for Computational Biology
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Journals
Conferences
- Pacific Symposium on Biocomputing Conference site with free full text proceedings.
- Intelligent Systems for Molecular Biology (ISMB) free online conference proceedings Also, the announcement for the 2008 conference
- RECOMB 2008 conference
- Rocky Mountain Regional Bioinformatics Meeting
Lecture-related web sites
- Introduction
- Molecular Biology Databases
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- 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.
- Database Search and Sequence Alignment
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- Various lecture notes on Dynamic Programming, from: GWU's computer science class
- A basic Java Applet demonstrating various sequence alignment algorithms
- BLAST
- Multiple Sequence Alignments
- Remember, none of these are optimal, so looking at the various different alignments they produce can be useful.
- Hidden Markov Models
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- 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.
- Sequence Assembly
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- The FASSI genome assembler
- The PCAP parallel genome assembler
- The Phusion assembler
- The PHRED, PHRAP and Consed Sequence read, assembly and finishing programs
- Gene Finding
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- GenSCAN (not to be confused with the commercial genEscan)
- HMMGene
- GrailEXP
- WEKA, a Java-based general machine learning package
- The Mammalian Gene Collection and RefSeq mRNAs. See also the related tracks on the Santa Cruz Genome Viewer, the NCBI list of full length cDNA resources, and their Consensus Coding Sequences project.
- RNA Genie predictor
- Protein Structure Prediction
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- PDB, the database of protein structures.
- Protein fold class databases. Each uses somewhat different definitions of a class
- The CASP site, including CASP6 and the not yet published CASP7
- LiveBench a continuous assessment of many fully automated prediction approaches
- Automated prediction servers you can use:
- Molecular Mechanics, Dynamics and Docking
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- The Amber Molecular Simulation Programs, including energy minization and molecular dynamics. $400 for Academic license
- The Charmm (or this version may be more up to date). The competitor from Harvard (Karplus's lab). $600 academic license. Another useful Charmm-related site from Charlie Brooks (see his home page for more useful information).
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- AutoDock (Open Source)
- FlexX, which has changed licensing terms recently, and is now $1500 for US academic users. A time-limited (8 week) license is available free.
- DOCK (free for academic use).
- 3D-DOCK suite, aimed at protein-protein interactions. Open source or free (beer) for academics.
- Mark Gerstein's movies of molecular dynamics. Try exploring the database of large scale molecular motions
- Arthur Olson's Autodock movies, and the Biotin binding to Streptavidin example.
- Computational Phylogeny
- Genetic Analysis
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- The Genetic Analysis Workshops
- Jurg Ott's Analysis of Human Genetic Linkage (third edition), the classic book in the field.
- A comprehensive bibliography of algorithms in linkage analysis
- North Shore Long Island Jewish Hospital's comprehensive list of (and links to) linkage analysis software
- The Human Haplotyping project (HapMap)
- Association analysis software:
- Microarrays
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- Affymetrix's web site, and particularly their "Scientific Community" section.
- Bioconductor, a powerful, open source collection of microarray analysis tools, written in the statistical language R.
- Wentian Li's exhaustive bibliography of expression array papers (click on the dates at the top of the page)
- Microarray data exchange and markup standards, MAGE and MIAME
- The AffyComp II comparison of Affymetrix GeneChip expression measures.
- The Visible Human. Doesn't really belong under expression arrays, but I mentioned it in clas...
- Molecular Mining's GeneLinker Platinum (now marketed by Improved OutcomesSoftware), including a use case and a downloadable demo
- Links and brief descriptions of microarray interpretation tools (pathway and coregulation)
- Biomedical Language Processing
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- Web-based BLP systems:
- BLP competitions:
- Our BLP tools:
