Internet Biology Resources

DNA Databases

Data Retrieval (Sequence Data)

• Human Genome Browser - Jim Kent's tool to browse the assembled human genome.
• Human Genome Browser-EMBL - Human and other Genomes Browser
• Mouse Genome Browser - Mouse and other Genomes Browser at UC Santa Cruz
• EMBL Sequence Retrieval - Online retrieval of DNA sequences - EMBL
• Entrez - Entrez Browser: NCBI
• LocusLink - Text search of curated sequence annotations.

Gene Feature Identification

• BCM Search Launcher - Collection of gene feature analysis tools
• GENIO/frame> - Frame shift analysis and sequencing error detection
• GENIE - Gene finder based on generalized hidden markov models
• GRAILExp - Gene prediction tool using BLAST to screen repeats
• NNSSP - Splice site prediction by neural network
• Splice Site Consensus - Consensus splice site sequence detection for human genes.

Homology Searches

• Biology Workbench - SDSC - Database searching by homology - free registration.
• BLAST - NCBI - Blast Server at NCBI.
• BLAST 2.0 - Japan - Blast Server in Japan (when NCBI is down or busy).
• WU-BLAST 2.0 - Germany - Enhanced Gapped Blast Server at EMBL
• WU-BLAST 2.0 - France - Enhanced Gapped Blast Server at Institute Pasteur
Documentation
• BLAST Docs: WU-BLAST 2.0 - Blast 2.0 information at Washington University
• GeneCover - Submit genbank accession number and get back all aligned ests.
• HomoloGene - Submit genbank accession number or locus name and get back members of orthologous cluster from other organisms.
• LOGO - LOGO display of concensus motifs in aligned sequences
• Motif - Search for motifs in DNA seqeunces. (Japan)
• PATSCAN - Search Genbank for matches to DNA Sequence Patterns
• RepeatMasker - Search your sequence for repeats and low complexity regions.

Multiple Sequence Alignment

• ClustalW - Japan - Best for alignment of global sequence similarity.
• CustalW - UK - EMBL server in the UK.
• CustalW - Singapore - Bioinformatics Institute server in Singapore.
• Dialign - For multiple sequence alignments of local sequence similarity, Dialign is superior to ClustalW.
Multiple Alignment Viewer
• Boxshade - France - View shaded regions of similarity.

Promoter Analysis

• COMPEL - Composite regulatory elements search.
• EpoDB - Erythropoiesis Gene Database - Includes transcription factor binding site annotations.
• GenomatixSuite - Search for distance-correlated transcription factor binding sites
• FunSiteP - Recognition and classification of eukaryotic promoters by searching tf binding sites using tf binding site consensi.
• GenLang - Search your sequence for protein coding gene structures.
• MatInspector Professional - Comprehensive search of genomic sequences for promoter/enhancer motifs - Free to academics with limitations.
• webMonkey - Evaluation of conserved transcription-factor binding sites.
• PatSearch - Search your gene sequence against Transfac and TRRD databases.
• Plant Transfac - Search your plant gene sequence against the Green Transfac database.
• ProScan - Search your sequence for promoter regions.
• Signal Scan - Search your promoter sequence for transcription factor binding sites using TFD or Transfac database.
• TESS - Search your promoter sequence for transcription factor binding sites.
• Transfac - Database of transcription factor weight matrices and tools.

Restriction Analysis

• REBASE UK - The Restriction Enzyme Database - UK Site
• WebCutter - Search your sequence for restriction sites online.

Sequence Submission

• Bankit - DNA Sequence Submission online - BankIt (NCBI) Server
• EMBL Sequence Data Submission - Online submission of DNA sequences - EMBL

Texts about Genes Online

• GENES - Online version of classic Lewin text. (free registration required first time)