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BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990). It is a very fast search algorithm that is used to separately search protein or DNA sequence databases. BLAST is best used for sequence similarity searching, rather than for motif searching. For searches using a query sequence of fewer than twenty residues, PatMatch is the best choice. (Go to PatMatch Search Page.) Another sequence alignment tool that may yield different results from BLAST, and may be useful for motif searching, is FASTA. (Go to FASTA Search Page.)
A fairly complete on-line guide to BLAST searching can be found at the NCBI BLAST Help Manual.
BLAST searches offered by SGD allow users to compare any query sequence to S. cerevisiae sequence datasets. To search other (non-yeast) datasets, NCBI BLAST can be used. To search fungal sequences, use SGD's Fungal BLAST tool.
Results of BLAST searches can be returned via web browser, or they can be sent to the user via email. SGD has a separate help document for the BLAST results page.
SGD offers these five BLAST programs to accommodate different types of searches:
SGD also offers a selection of sequence databases that can be searched, depending on the user's requirements.
Sequences can be submitted for a BLAST search in two different ways. The sequence can be uploaded from a local text file with FASTA, GCG, or RAW formatting, or the sequence can be typed or pasted into the Query Sequence window. (Note: The contents of an uploaded sequence file will not be displayed in the Query Sequence window of the search page.)
To use the Upload Local File option:
BLAST search results can either be returned directly to the user's web browser, or via email. Results returned via email are available in three forms: URL (the web address at which the results can be found is mailed to the user); HTML (the BLAST output is sent in HTML format, for local viewing on the user's web browser); and TEXT (the BLAST output is returned as normal text, with no HTML formatting).
If a BLAST search results in no, or few, matches, the user may try to increase the number of matches in a number of ways. Going back to the BLAST search page, one can change the database searched, change the protein comparison matrix, or increase the number of alignments shown. Sometimes, performing a FASTA search can provide a different result.
Changing other options can also change the outcome of the BLAST search. The Expect threshold ("E") reflects the number of matches expected to be found by chance. If the statistical significance of a match is greater than the Expect threshold, the match will not be reported. The E threshold default is set to 10. Decreasing the E threshold will increase the stringency of the search: fewer matches will be reported. On the other hand, increasing the E threshold will decrease the stringency of the search and result in more matches being reported. If a query sequence is short (less than about 30 residues), the user will want to adjust the Cutoff Score ("S") to a lower value, which will result in a less stringent criterion for reporting matches. The user can also change the word length (W): BLAST first searches for a perfect match of at least the word length. Once a match is found then it tries to extend the high-scoring segment pair (HSP). The default W value for BLASTN is 11; for all other programs the default is 3. If the word length is less than 11 the query sequence must be less than 5000 bp.
BLAST searches are also subject to filtering. A filter will remove repetitous sequences from a query, so that the results of the BLAST search will be less numerous and, ideally, more informative. For nucleic acid query sequences, the "dust" filter is used as the default. For all other searches, the "seg" filter is the default. You can always use the "Filter options" pull-down menu to select a different filter option or to remove filtering entirely (select "none").
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