Bioinformatics in the Classroom

Lots of Links

Lists of Links ABIM Sullivan Symposium ABIM Centers Baylor College of Medicine: BCM, Human Genome Sequencing Center (BCM Sequence Utilities) BIOSCAN E. coli Genome Center, University of Wisconsin-Madison. European Molecular Biology Laboratory:EMBL European Bioinformatics Institute: EBI ExPASy Genome Net WWW server Japan Harvard Biological Laboratories Johns Hopkins University Lawrence Berkeley Laboratory Human Genome Center Lawrence Livemore National Laboratory's Biology: LLNL National Center for Biotechnology Information: NCBI National Center for Genome Resources: NCGR National Institute of Health: NIH NIH GenoBase DataBase GateWay: BIMAS SEQNET SRS Stanford Human Genome Center: SHGC The Sanger Centre Weizmann Institute of Science Genome and Bioinformatics Whitehead Institute for Biomedical Research/MIT Center for Genome Research Entrez Databases Multiple Organisms GENBANK EMBL DDBJ Inherited Disease Genes Identified by Positional Cloning The Expressed Gene Anatomy Database: EGAD Sequence Elements EPD Eukaryotic promoter database PROSITE The CpG Isle database TRANSFAC Transcription factor database Genome Organism Overview of Genome Sequencing Projects Terry Gaasterland ACEDB (Sanger) ACEDB C.Elegans (AGIS) BSORF: Bacillus subtilis (Japan and PasteurInstitute, France) Cyanobase Synechocystic sp., Kazusa DNA Research Institute, Japan DictyDB--The Soil Amoebae Dictyosteliusm discoideum E.coli K-12 Genome Sequence, Wisconsin-Madison University E.coli Databank, NIST (Japan) FlyBase: A Database of the Drosophila Genome Human Genome DataBase GDB Human sequences collections, UniGene, NCBI MBGD - Microbial Genome Database, HGC, Univ. of Tokyo Mouse Genome Database: MGD MycDB -- Mycobacteria Pyrococcus horikoshii OT3 Database, NITE, Japan PathoGenes--Fungal pathogens of small-grain cereals Rat Genome DataBase Saccharomyces Genome Database (Stanford) The TIGR Microbial Database The TIGR Arabidopsis Thaliana Database The TIGR Mouse Gene Index: MGI Organism Classification The TIGR Microbial Database The TIGR Arabidopsis Thaliana Database The TIGR Mouse Gene Index: MGI Genome DataBase GDB UniGene Human sequences collections Saccharomyces Genome Database ACEDB (Sanger) ACEDB C.Elegans (AGIS) DictyDB--The Soil Amoebae Dictyosteliusm discoideum MycDB -- Mycobacteria PathoGenes--Fungal pathogens of small-grain cereals The Mouse Genome Database: MGD The Rat Genome DataBase FlyBase: A Database of the Drosophila Genome Training Sequence Benchmark Sequences from Banbury Cross Sequence Test Set (Roderic Guigó i Serra) Bibliography Libraries Global Bioinformatics New Service. Computational Gene Recognition Bibliography. PubMed Retrieval System Free MEDLINE. BIO-JOURNALS/bionet.journals.contents Table of Contents Archive and Search. Search Bio-wURLd for your favourite URL. Clio server at CSHL Cold Spring Harbor Laboratory Press. The NIH Grant Database Search Biologists Search Palette Medline Search, Protein Database search, Nucleotide Database search, dbEST Search Searchable Gopher Index: Biology-journal-contents Searchable Gopher Index: Bibliography on sequence analysis Electronic Journals Bioinformatics (former CABIOS) on Line Cell on Line. EMBO J on Line Gene Combis Computing for Molecular Biology Information Service (TM). Genome Research on Line JBC on Line NATURE on Line NAR on Line SCIENCE on Line Other Journals Molecular Vision A peer-reviewed journal of Molecular and Cellular Vision Research Oxford University Press (OUP) Springer Journals Preview Service (SVJPS) Academic Press Journals Gopher Menu Bio/Chemical Journals from Pedro's BioMolecular Research Tools Courses, Workshops, News ADVANCED GENOME SEQUENCE & ANALYSIS Course WWW Virtual Library: Biomolecules BioMOO Electronic Conference transcript with invited lecturer William R.Person. Human Genome News

Web Servers Predicting Gene Structure AAT (Analysis and Annotation Tool for Finding Genes in Genomic Sequences) Michigan (USA) CDS (Search Coding Regions), Pasteur (France) EcoParse (mailserver for finding genes in E. coli DNA) Info (Denmark) Eukaryotic Promoter Prediction by Neural Network LBNL (USA) FramePlot NIH-NET (Japan) Gene Finder, (Human, Mouse, Arabidopsis, Fission Yeast) CSHL (USA) GeneID-3 Search Form IMIM, Barcelona, (Spain) Genie (gene finder based on Hidden Markov Models) LBLN (USA) GenLang (tRNA, group I intron, protein gene : "Linguistic Methods") CBIL Pennsylvania (USA) GenScan (Identification of complete gene structures in genomic DNA) Stanford (USA) GenView (Protein-Coding Gene Prediction) ITBA (Italy) GRAIL ORNL Oak Ridge (Exons, repeats, Poly A sites, CpG) (USA) HCpolya (Hamming Clustering poly-A prediction in Eukaryotic Genes) ITBA (Italy) HCtata (Hamming-Clustering Method for TATA Signal Prediction in Eukaryotic Genes) ITBA (Italy) NetGene2 CBS (Denmark) NetPlantGene V2.0 (neural network predictions of splice site prediction in Arabidopsis thaliana DNA) CBS (USA) ORF Finder (graphical analysis tool) NCBI (USA) ORFGene (Gene Structure Prediction using Homologous Proteins) ITBA (Italy) PredictGenes CBRG Zurich (Switzerland) Procrustes WWW server Gene Recognition via Spliced Alignment, USC (USA) Proscan II (predicts putative eukaryotic Pol II promoter sequences) University of Minnesota, (USA) Putative DNA Sequencing Errors Check EMBL-Bork (Germany) RecSta (coding region (CDS or exon) prediction program using COA) Lyon (France) Splice Site Prediction by Neural Network LBNL (USA) SpliceView (Splice Prediction by using Consensus Sequences) ITBA (Italy) tRNAscan (Search for transfer RNA genes in genomic sequence) Washington (USA) Molecular Biological Server Variety of tools; Laboratory of Theoretical Genetics, Novosibirsk, Russia Blast Arabidopsis (blastn, tblastn, tblastx, blastp, blastx) Stanford, (blastn, tblastn) St Louis Aspergillus nidulans (blastn, tblastn, tblastx) Oklahoma dbEST, NCBI's EST (blastn, tblastn, tblastx) CBIL C.briggsae (blastn, tblastn) St Louis C.elegans (blastn, tblastn, tblastx, blastp, blastx) Sanger, (blastn, tblastn) St Louis, EST (blastn, tblastn) NIG Complete Genomes (blastp), BMERC Drosophila (blastn, tblastn, tblastx, blastp, blastx) (Berkeley), BDGP, (blastn, tblastn, tblastx, blastp, blastx) EBI E.coli (blastn) Alces, (blastn, tblastn) ECDC Fugu rubripes (blastn) HGMP Human (blastn, blastx) Sanger, (blastn, tblastn) St Louis HIV (blastn, blastx, tblastn, blastp tblastx, blast3) IGS, (blastn, blastx, tblastn, blastp) Stanford Microbial genomes (NCBI) (tblastn, blastn) TIGR M.leprae (blastn, tblastn, tblastx), Sanger M.tuberculosis (blastn, tblastn, tblastx), Sanger Neisseria gonorrhoeae (blastn, tblastn, tblastx), Oklahoma N.meningitidis (blastn, tblastn, tblastx), Sanger Parasite (blastn, tblastn, tblastx) EBI Pseudomonas aeruginosa NCBI (tblastn, blastn, blastx) NCBI P.falciparum (blastn, tblastn, tblastx), Sanger S.cerevisiae (blastn, tblastn, tblastx), Sanger, (blastn, tblastn, tblastx, blastp, blastx) Stanford S.coelicolor (blastn, tblastn, tblastx), Sanger S.pombe (blastn, tblastn, tblastx), Sanger Streptococcus pyogenes (blastn, tblastn, tblastx) Oklahoma Synechocystic sp.(blastp, blastn) Kazusa Yeast (tblastn, blastp) Alces Miscellaneous Servers CENSOR Web Server aligns sequences against a reference collection of human or rodent repeats, Genetic Information Research Institute, Palo Alto, California Dst Alces internal human repeats (Minnesota) Dot Plot Alces internal repeats (Minnesota) Prodom with Blast INRA Toulouse (accès par e-mail) Repeat Masker screens DNA sequences in fasta format against a library of repetitive elements (University of Washington) Software Commercial Packages DNASTAR GCG: The Wisconsin Package Software GENQUEST OMIGA PCGENE compatible (Oxford Molecular Group Product) BIONET online service (Oxford Molecular Group Product) GENESEQ A Protein and Nucleic Acid Database (Oxford Molecular Group Product) Miscellaneous Packages DELILA (Logos) EGCG: (Sanger) GLIMMER: Gene Locator and Interpolated Markov Modeler. (A system for finding of genes in microbial DNA) H2W WWW interface to the GCG Sequence Analysis Software Package Annotation Gene family experts - these researchers are willing to provide assistance in the annotation of certain genes Exon prediction analysis - how well do commonly used algorithms work? Methods for identification of transposons, solo LTRs, and other genomic repeats Scheme for naming genes encoded on the BAC clones   Annotation References and Bibliography We use compositional and comparative methods in the analysis of genomic DNA sequence. The comparative methods primarily involve searches for homology within publicly available databases and multiple sequence analyses generated locally. Compositional analysis is concerned with the construction of gene models from computer-predicted exons and exon-splice sites. Database Searching Gapped BLAST at NCBI BLAST via AtDB FASTA - available at AtDB Smith-Waterman SSEARCH Motif searching PROSITE from SwissProt database BLOCKS PRINTS Pfam ProDom Transmembrane domain predictions at Baylor College of Medicine Exon prediction and gene modelling programs GenScan GRAIL MZEF NetPlantGene tRNA predictions are performed with tRNAScan-SE Click here for a detailed discussion of our method for identfying putative autonomous and non-autonomous transposons, solo LTRs, and LINEs. Short tandem repeats or microsatellites are located with RepeatMasker. Local manipulations of the sequence are performed with the GCG package. Multiple sequence analysis is also performed with CLUSTALW. Resources for Arabidopsis phenotypes include Arabidopsis Information Management System (AIMS) and Nottingham Arabidopsis Stock Centre (NASC). The Kyoto Encyclopedia for Genes and Genomes (KEGG) is a good resource for metabolic pathways. We also utilize NCBI's Entrez to gather relevant information. Various scripts written in-house are also used. And some good old fun at http://jura.ebi.ac.uk:8765/ext-genequiz/genomes/dm0006/ Mesquite: a modular system for evolutionary analysis; a new tool from the makers of the Tree of Life Does genome size matter? One place to ponder this question is the Animal Genome Size Database, where a zoology graduate student has been compiling tables of all animal genomes for which he can find data. Look up chromosome numbers and genome sizes ("C-values") for over 2900 vertebrates and invertebrates, from spongi to Homo sapiens. Includes links to similar sites for animal and plant genomes.