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EBI 2Can Tutorials Protein and Proteomic Analysis

2Can Support Portal - Protein and Proteomic Analysis

BLAST similarity search <<< 2/12 >>>

Running a WU-BLAST2 BLAST search


WU-BLAST2 stands for Washington University Basic Local Alignment Search Tool Version 2.0.The emphasis of this tool is to find regions of sequence similarity quickly, with minimum loss of sensitivity. This will yield functional and evolutionary clues about the structure and function of your novel sequence. Dr Warren Gish at Washington University released this first "gapped" version of BLAST allowing for gapped alignments and statistics.

We will consider a peptide/protein sequence, sequence 7, and look for peptides/protein sequences that are similar in UniProt. This peptide/protein sequence is a real entry in this database, so we will expect to find a sequence that is a perfect match to our test sequence. Also we expect to find similar peptide/protein sequences, perhaps from closely related animals, or from sequences for closely related proteins.

Consider the following WU-BLAST2 submission form:


Go to the main EBI website

N.B. This tool can also be programmatically accessed as a web service.

  • The sequence, sequence 7 is entered into the textbox in FASTA format, which consists of a one-line header starting with a ">" symbol, followed by the sequence name. The sequence is then entered on new line(s). You can find out more about sequence formats here.

  • The title of the search is left as "Sequence" although you can give your search title any name you wish to help you identify the results.

  • "Interactive" is chosen so that the results will be delivered to the browser as soon as they are available. Alternatively you can chose "email" and fill in your email and have the results delivered via email.

  • The Wu-BLASTp program is used, which is designed to search a protein query sequence against a protein databank, in this case UniProt complete and non-redundant protein sequence collection is selected.

  • The number of scores (hits to the database) is limited to 10 and the alignments of these against the query sequence to 5, to limit the size of the output results.

  • Other options have been left on "default"

  • You now can either go to the WU-BLAST2 page and run the search yourself or view the sample results for sequence 7.

  • Which protein does this sequence code for?

See the results of this BLAST search >>>

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