Genome and Gene analysis

Contents of this page:

GeneMap 98 (Science98)

The fastest links (in UK) are in bold. Use these unless you are prepared to wait...

Database Centres

• Sequence retrieval
• Search at the Sanger Centre for SWISSPROT SWISSNEW PIR EMBL EMNEW NRL3D TREMBLNEW GBRNA SPTREMBL IMGT SBASE (Sanger home)
• Search EBI for most of the above plus others (EBI home)
• Search HGMP for most of the above plus GENBANK GBNEW (HGMP home)
• Search EMBL for most of the above plus GENBANK NRL3D TREMBL TREMBLNEW
• Search worf for just about anything you need...including GENPEPT!
• Similarity searching and the like
 
• BLAST or PSI-BLAST at NCBI
• ...or do a BLASTN or BLASTP search using worf! (worf home)
• BLITZ and Bic-SW FASTA3 search at EBI
• Compugen's accelerated search servers: SW at EBI; SW, FastA and Blast at Weizmann
• TimeLogic's accelerated Smith-Waterman or FRAMESEARCH (at least get your free GeneCodes mousemat!)
• RepeatMasker at Washington U!
• Get reports from the TIGR Human Gene Index or do a Sequence search there
• NCBI-Genbank
• Vertebrate Comparative Database at HGMP
• OMIM at HGMP or NCBI
• CEPH
• LDB; The Location DataBase at Southampton
• Baylor College of Medicine Search Launcher
• Whitehead Institute. The mirror at HGMP is not available (at the moment)
• Search for a marker by name at Whitehead
• GDB; use the mirror at HGMP.
• Sequences over 100 kb
• Protein Sequence Databases...
• Human Gene Mutation Database
• IMGT, the international ImMunoGeneTics database at EBI or CNRS
• Other Genome Databases...
• Cytokine cDNA database
• BodyMap: Anatomical Expression Database of Human Genes

Other Genome Centres

• ANGIS - The Australian National Genomic Information Service!
• Lawrence Livermore National laboratory Human Genome Center
• Los Alamos Center for Human Genome Studies
• The Cooperative Human Linkage Center
• HGMIS at Oak Ridge Laboratories
• BioScan at UNC-Chapel Hill
• Molecules R Us at NIH
• Nucleic Acids Database Project (Rutgers)
• GenoBase at NIH
• Molecular Genetics Labs at CSMC
• The Institute for Genomic Research (TIGR)
• Various programs at the Virtual Genome Centre at UMN

Gene Mapping Stuff...

• Mouse Genetics and Man-Mouse homology at Harwell
• Genome-wide scans from Todd's Lab
• The Fugu homepage...
• Molecular Biology at NIH
• STS map of the whole genome
• GeneServer Archives at Houston
• Houston FTP server
• Whole Genome Radiation Hybrid Panel
• EST Trace Data
• Gene Prediction software:
• A Bibliography of Computational Gene Recognition
• GeneID
• The GeneFinder suite: Old site or the New site(WWW)
• GeneHunt at EBI
• Gene Parser (download UNIX binary)
• Genie. (Splice site finder) (Genie Home) (WWW)
• GenLang. (GenLang Home)
• GENSCAN (WWW)
• Grail (WWW or download binary)
• MZEF (WWW or UNIX binary)
• WebGene (WWW)
• MORGAN: A decision tree system for finding genes in vertebrate DNA (UNIX source)
• PROCRUSTES (WWW)
• SorFind (DOS executable) and others from IUBIO, Indiana
• VEIL: A hidden Markov model for finding genes in vertebrate DNA (Unix binary)
• Xpound
• Banbury Cross
• AAT- Analysis and Annotation Tool (WWW or email)

Sequence Analysis and Protein Structure Servers...

• PEST Server at iub-jena
• PSORT: Cellular localisation of your protein!
• Transcription Element prediction:
• Matrix Search
• TFSearch
• TESS
• FastM and ModelInspector TF site finder at GSF in Germany
• Structural Classification of Proteins Server at MRC-LMB
• Analysis of protein 3D structures (Cambridge)
• Swiss-Model - an automated knowledge-based protein modelling server
• BCM Sequence Annotation Server
• BCM Secondary Structure Prediction Server
• PREDATOR secondary structure prediction fo single and multiple sequences
• WebCutter:get a restriction map for your DNA sequence!
• Brookhaven Genome Sequencing Facility
• Michael Zuker's RNA page 
• POLYAH, TSSG and TSSW Recognition of human PolII promoter region and start of transcription
• Find TATA Signals, Splice sites, ORF and Poly(A) predictions using WEBGENE at CNR in Milano! (Java)
• Eukaryotic Promoter Database at Lausanne
• The PredictProtein Server at Heidelberg
• PROSITE pattern search at EBI
• BLOCKS WWW server
• Protein Structure Prediction Servers on the Web
• ProDom server at INRA

Multiple Sequence Analysis

• Sequence alignment and modeling server at UCSC Computational Biology Group
• AMAS - Analyse Multiply Aligned Sequences
• The Match-Box server; a web-based Multiple alignment server!
• MSA, Calculating Multiple Alignments
• AllAll: Calculate Phylogenetic Trees, Alignments and a lot more
• Protein Sequence Alignment and Database Scanning, by Geoffrey Barton
• 3D-Ali Information File (Daresbury)
• 3D-ALI Database Interface
• The PredictProtein server, utilizing MaxHom Alignments
• Tom Schneider's Sequence Logos
• PSORT - Predict Protein Sorting Signals Coded in Amino Acid Sequences
• BCM Searches and Utilities Launcher

Human Chromosome-specific pages

• Full list list maintained at HGMP
• Chromosome 1
• Chromosome 7
• Chromosome 6
• Chromosome 9
• Chromosome 20
• Chromosome 22
• Chromosome X Virtual Workshop

Other WWW servers...

• Hum-Molgen page
• Comprehensive Biosciences Index from Harvard
• ExPASy Molecular Biology Server
• Internet Directory of Biotechnology Resources
• World Health Net
• New WWW sites from Hum-Molgen, Hugo, etc...

Commercial Stuff...

• Biotech Company WWW Registry
• Amersham
• Boehringer Mannheim
• Cambridge BioScience
• Compugen inc.
• Derwent - Gene Therapy, Patent and other data
• Eppendorf
• Gemini's Biopages - Exhibition Site for the Biomedical Sciences and Lab Product Data
• interLAB - information about laboratory equipment
• InVitroGen Inc.
• ICN Pharmaceuticals
• Millipore catalogue
• Molecular Dynamics
• New England Biolabs
• New England Nuclear
• Perkin Elmer
• Promega
• Research Genetics
• TimeLogic inc.




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This page is constantly being revised.
Please send any good ideas for changes or additions to this list to me.
John Broxholme

This groovy background was found at Washington/Merck's pages
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