BLAST search in Uniprot
Data access component allows for BLAST searches in the Uniprot database. The query is chosen from the display or sequence viewer. Alternatively, a local sequence file can be used. If it contains multiple sequences, the first one will be used as the query. Also, the user should specify what the sequence should be treated as: protein or DNA.
In addition, basic BLAST parameters, such as cutoff e-value, similarity matrix, level of sensitivity, can be adjusted via the Settings option. Finally, the user may limit the number of returned hits by using a pulldown menu. The maximum number is 100.
The search normally takes under one minute, but the exact time depends on the size of the sequence and parameters, such as cutoff value and maximum number of hits. Once the search is completed, the list of hits is displayed. The view shows name, accession number, description and e-value for each hit. The user may select a single result of multiple hits and load them into the sequence viewer. In addition, it is possible to view the local alignment of each hit produced by BLAST. Finally, the raw BLAST output file may be saved locally.