BLAST stands for Basic Local Alignment Search Tool. It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterised genes. The emphasis of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of this novel sequence. Regions of similarity detected via this type of alignment tool can be either local, where the region of similarity is based in one location, or global, where regions of similarity can be detected across otherwise unrelated genetic code.

The EBI provide the only BLAST libraries to use the IPD-IMGT/HLA Database. The BLAST tool searches against the nucleotide and protein sequences of HLA alleles and related sequences included in the database. Currently the nucleotide library only includes the coding sequences, we are working towards providing a genomic BLAST library as part of this site.

The EBI BLAST engine is now automatically configured for IPD-IMGT/HLA searches when you access it directly from this page. If you are accessing the page from another location or wish to alter the parameters provided please read the guidelines below.

1) Selecting a BLAST engine

The first step is to select the type of search required. In the right-hand side of the table under the "OTHER TYPES" select Nucleotide or Protein Databases, this defines the databanks available for searching.

2) Selecting a database

The IPD-IMGT/HLA sequences are only available from IPD-IMGT/HLA Databases in BLAST. The component entries are available from the EMBL-Bank Databases. The cDNA nucleotide sequences can be found under the IMGT tab, and then under the "IMGT/HLA (cds)" option. The gDNA nucleotide sequences can be found under the IMGT tab, and then under the "IMGT/HLA (genomic)" option. The protein sequences can be found under "Other Dataases" and the "IMGT/HLA" option. These databases contain all the sequences in the current release of the IPD-IMGT/HLA Database.

If the menus do not automatically update when different BLAST programs are chosen, this is most likely a local browser problem. There have been some reported problems with Internet Explorer. The general advice is to try reloading the page first, then try a "shift"-reload, if this still does not work, exit the browser and start again.

3) Entering a sequence

The sequence can be entered using either a "cut & paste" method or the file upload option. The sequence should ideally be in FASTA format. This means a single sequence with the first line starting with a greater than sign (>). The rest of this line is used to name the sequence and can contain spaces but should not contain numbers or any form of formatting i.e. asterisks (*) or periods (.) as BLAST considers these invalid nucleotides. The IUB (International Union of Biochemists) codes are acceptable in a BLAST search, however, if the sequence contains more than 50% ambiguity codes it will mostly likely be rejected, but if successful may contain false positive hits which are of limited use.

The BLAST engine is designed for searching for sequence similarities over large sequences. Searching the databases with short sequences may result in an error. The minimum length is 11 bases, however the recommended minimum sequence length is 22 bases (nucleotides/blastn) or 6 amino acids (proteins/blastp). Some searches under this recommended size may run but even single mismatches can cause the search to fail.

4) Search Errors

Searching for any matches to intron sequences will result in an error. The IPD-IMGT/HLA does not currently contain any intron sequence and so these are not available through the BLAST engine. The BLAST engine can currently only search coding sequence. If you need to search for intron sequence the EMBL database should be used until the IPD-IMGT/HLA Database incorporates intronic sequence.

The BLAST scoring system can sometimes distort the results for example a 546 base pair sequence of ~95% identity may score higher than a shorter (270 bps for example) sequence of 100% identity. Therefore the top results may not always be the best match. This is due to the high degree of similarity between HLA sequences

The WU-Blast programs are the Washington University version of the BLAST algorithms. The links in the output files are to the IPD-IMGT/HLA flat files. To view an alignment of your BLAST search use the "View using Mview" option on the output screen.

Further Information

For more information about the database, queries (including website) or to subscribe to the IPD mailing lists please contact IPD Support.

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