From:www.mdbbs.org
Molecular Biology Databases
- NCBI GenBank
- EMBL
- EMBL - InterPro - Database of protein families, domains and functional sites
- Swiss-Prot and TrEMBL
- Protein Data Bank (PDB)
- UniProt Universal Protein Resource
- OWL Composite Protein Sequence Database
- dbEST cDNA Fragments
- PIR Protein Sequence Database
- TRANSFAC - Gene regulation database
- TIGRFAMs - TIGR protein families db
- Nucleic Acids Research Molecular Biology Database Collection
- Nucleic Acids Research 2005 Organismal Database Issue
- ExPASy's Species Specific Databases
- DBCAT - Public Catalog of Databases
- OMIA - Online Mendelian Inheritance in Aminals
- OMIM - Online Mendelian Inheritance in Man
- MGI - Mouse Genome Informatics
- Yeast Genome Page
- FlyBase - Database of the Drosophila Genome
- The Interactive Fly
- Wormbase - C. elegans Data Base
- tair - Arabidopsis Information Resource
- MIPS - Arabidopsis Data Base
- GeneCards
- GenomeWeb - Protein interaction databases
- BIND - Biomolecular Interaction Network Database
- DIP - Database of Interacting Proteins
- MINT - Molecular INTeraction database
- MIPS - Mammalian protein-protein interaction database
- Blast Server
- NCBI Blast tutorial
NCBI Psi-Blast tutorial - Geospiza Blast tutorial for beginners
- Fasta Server
- Motif Search - Kyoto University Bioinformatics Center
- ScanProsite
- InterProScan
- BLOCKS
- PRINTS
- ProDom
- Pfam
- SMART - Simple Modular Architecture Research Tool
- Panther - Protein analysis through evolutionary relationships
- MEME - Motif building
- MAST - MEME motif matching within a protein database
- PROSITE - Build a motif and search
- PROSITE - Generate a prosite or HMMer profile from a multiple sequence alignment
- PROSITE - E nter a sequence and search for prosite, blocks, prodom, prints and pfam motifs
- DomainFinder
- Dialign T
- Chaos-Dialign
- Anchored Dialign
- ClustalW - Software Source
- ClustalW - Alignment submission form
- T-Coffee - Multiple sequence alignment
- Divide and Conquer Multiple Sequence Alignment
- Muscle - Multiple protein sequence alignment at Berkeley
- Squint - Multiple sequence alignment editor
- GeneDoc - Sequence alignment editing software
- Decrease redundancy - Reduces a set of sequences to a non-redundant set
- Cinema - Color INteraction Editor for Multiple Alignments
- AltAVisT - Alternative alignment visualization tool
- Balibase - reference sequence database for studying alignments
- ExPASy Proteomics tools
- EMBL Database searching, browsing and analysis tools
- ProteinPredict Server
- NCBI Molecular Tools
- EBI Tool Box
- Molecular Toolkit
- Mathworks Sequence Analysis Tools
- CMS Molecular Biology Resource
- SAPS - Statistical Analysis of Protein Sequences
- ProtParam
- ProtScale
- PatScan Pattern Scanning
- VAST - Search for a protein's structural neighbors
- Biology WorkBench
- Swiss-Shop - automatically obtain by e-mail new sequences of interest
- RandSeq - Random protein sequence generator
- HMMER - Hidden Markov Modeling; HMMER Documentation
- PubMed - Entrez
- Pedro's Biomolecular Research Tools
- SeqAnalRef
- Agricola
- iHOP - Links to literature on individual proteins
- Biological Journals and Abbreviations
- Computational Molecular Biology at NIH
- Bioinformatics Servers
- Computational Biology at Argonne National Laboratory
- Baylor University College of Medicine HGSC
- Bielefeld Bioinformatics Server
- MIPS - Munich Information Center for Protein Sequences
- GOBICS - University of Goettingen Bioinformatics Server
- PhyCom - A Phylogenetic Community
- Rod Page's Server at Glasgow
- University of Oxford evolutionary biology group
- Allan Wilson Center - New Zealand
- Molecular Dynamics Simulations -- Tutorial
- [url=http://bmerc-www.bu.edu/]Boston University (BMERC) Protein Sequence Analysis (PSA)[/url]
- UC Santa Cruz sequence alignment and modeling system (SAM)
- NIH Molecular Modeling Home Page
- Molecular modeling toolkit
- Molecular modeling of proteins
- nMOLDYN
- MEGA3
- MrBayes
- Beast
- PAML
- PAUP - home page; Quick Start Tutorial
- Brian O'Meara Paup tutorial
- Weighbor - Weighted neighbor-joining
- PHYLIP
- Spectronet - visualization of non-bifurcating tree like complex evolutionary data
- Mesquite - Modular system for evolutionary analyses
- Tree-Puzzle - maximum likelihood analysis of sequence data
- SplitsTree4
- McClade
- Clann - Constructing supertrees
- DAMBE
- HYPHY - maximum likelihood analyses of genetic sequence data
- PHYML - fast algorithm for phylogeny estimation using maximum likelihood
- ModelGenerator - amino acid and nucleotide substitution model selection
- FitModeL - fits substitution models to sequence data using maximum likelihood
- PROTTEST - selection of best-fit models of protein evolution
- Rose - Random model of sequence evolution
- Phyl-o-Gen - Phylogenetic simulation package
- Seq-Gen - Monte Carlo simulation of sequence data along phylogenetic trees
- Rhino - Phylogenetic models for estimating rates and dates
- Pebble
- The Tree of Life
- Treeview
- Time Tree of Life
- Glossary of terms used in phylogenetic reconstruction
- Multiple regression
- Factor analysis including principal components analysis
- Structural equataion modeling
- Discriminant analysis
- Molecular Biologists Desk Reference
- Codon Usage Tables
- ExPASy BioHunt Search
- Tree Thinking Group - Phylogenetic analysis in education
- Molecular Biology and Evolution
- Journal of Molecular Evolution
- Evolutionary Bioinformatics Online
- PLOS Computational Biology
- Computational Biology and Chemistry
- Bioinformatics
- Nucleic Acids Research
- BMC Bioinformatics
- Journal of Bioinformatics and Computational Biology
- Journal of Molecular Modeling
- Journal of Computational Biology
- BMC Evolutionary Biology
- Journal of Negative Results -- In case your experiment doesn't work out like you had hoped
- YouSendit - Very useful server for e-mailing very large files
- RefDesk - World's greatest source of facts and links
- ISI Web of Knowledge
- Society for Molecular Biology and Evolution
- International Society for Computational Biology
- Society of Systematic Biologists
- Cosmic Evolution
- Evolution Resources from the National Academies
- BioMed Central
- The Onion
- Trivia - For stuff not covered in our GN/ST 756 course
- SCIgen - Automatic paper generator for those losing out in the publish or perish rat race.
- Bill Atchley's Home Page
- Bill Atchley's Personal Links Page
- Jeff Thorne's Home Page
- Jeff Thorne's Favorite Website
- NCSU Library
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