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BIOINFORMATICS WEBSITES

Step 1: Obtaining a sequence of interest

  • PubMed Search PubMed, a public version of full Medline for topics of interest (US)
  • GeneBank Search Genbank for sequences of interest (US)
  • ATLAS Search protein and nucleic acid databases using Atlas at MIPS (Germany) - Sequence Database Access
  • SRS Search a variety of sequence and structure databases using the SRS server at EMBL (Germany)
  • DBGET Search a variety of sequence and structure databases using the DBGET server at Kyoto (Japan)

    Step 2: Identify ORFs and translate into protein

  • GeneFinder at the Sanger (UK)
  • GENSCAN at MIT (US)
  • GRAIL at ORNL (US)
  • DNA sequence translation page at the University of Minnesota (US)
  • Gene feature searches at Baylor College of Medicine (US)
  • GenLang searches at University of Pennsylvania (US)
  • DNA sequence translation into protein tool at ExPaSy (Switzerland)
  • AAT at Michigan Tech University (US)

    Step 3: Find similar sequences in the databases

  • Nucleotide sequence Search the database of your choice using Blast at NCBI (US). Use the blastx option
  • Protein sequence Search the database of your choice using Blastp + Beauty at Baylor College of Medicine (US)
  • Protein Sequence Search the database of your choice using the BIOCCELERATOR at the Weizmann Institute (Israel)

    Step 4: Do a global alignment of your sequence vs similar sequences - may help getting a better insight about your target sequence (eg. 'gain' or 'loss' of functional domains vis-a-vis a reference sequence

  • Pairwise Sequence Alignment at EERIE, France
  • Pairwise Sequence Alignment query at Baylor College of Medicine (US)

    Step 5: Look for gene family

  • Multiple Sequence Alignment query at Baylor College of Medicine (US)
  • AMAS Analyze multiple sequence alignments at the AMAS at Oxford University (UK)
  • BOXSHADE Get visual information about the aligned regions at the BOXSHADE server at ISREC (Switzerland)
  • CLUSTAL Multiple Sequence Alignment with phylogenetic tree capabilities using CLUSTAL at EBI (UK)

    Step 6: Look for the presence of specific patterns in your protein

  • Concensus server Extract a concensus matrix using the concensus server at Universite Libre de Bruxelles (Belgium)
  • ProfileScan Search the Procite library using the ProfileScan server at ISREC (Switzerland)
  • Blocks Search the Blocks database at Fred Hutchinson Cancer Research Center (US)
  • Motif Search Database using Motif at GenomeNet (Japan)
  • PatScan Look for a pattern you define using PatScan at Argonne National Laboratories (US)
  • Psort Predict protein sorting signals using the Psort server at the Institute for Molecular and Cellular Biology, Osaka University
  • Display Generate a concensus from your alignment using Display

    Step 7: Find similar sequences in other species

  • FASTA Search several proteomes using the FASTA search interface at the University of Virginia (US)
  • WU-BLAST2 Search the SGD (S. cerevisiae) Database using the WU-BLAST2 at Stanford (US)
  • TAIR Search the AtDB (A. thaliana) Database using the TAIR Database Search
  • Fly BLAST Search the Drosophila Genome Project sequences using the Fly BLAST search feature at EBI (UK)
  • BLAST Search several species-specific databases with Blast at NCBI. Use the pull-down menu to select species-specific database

    Step 8: Determine the putative structure of your protein

  • SIMPA Predict the secondary structure of your protein using the SIMPA server at the NIH
  • GOR Secondary Structure Prediction Predict the secondary structure of your protein
  • Quadratic Logistic Secondary Structure Prediction Predict the secondary structure of your protein using Quadratic Logictic SS
  • PredictProtein Predict the secondary structure of your protein using PredictProtein server at the EMBL (Germany)
  • NNPREDICT Predict the secondary structure of your protein using NNPREDICT at the University of California
  • PPSP Predict the secondary structure of your protein using the PPSP server at Baylor College of Medicine
  • COILS Look for coil-coil regions using the COILS server at ISREC (Switzerland)

    Step 9: Obtain information about function of related proteins

  • PubMed

    To understand the function of your target protein, it may be useful to gather information about protein that share similar structural or sequence elements. Thus, a PubMed search using as keywords the names of the proteins revealed by the various steps of this analysis, may provide you with functional insight about your protein

    Step 10: Input your sequence into an "alert" server

    "Alert" servers will send you a message if a sequence similar to yours has been inputed in a database. Choose from the following servers:

  • Sequence Alerting at the EMBL (Germany)
  • SSWISS-SHOP server at ExPaSy (Switzerland)