BLAST: at the core of a powerful and diverse set of sequence analysis tools

Abstract

Basic Local Alignment Search Tool (BLAST) is one of the most heavily used sequence analysis tools available in the public domain. There is now a wide choice of BLAST algorithms that can be used to search many different sequence databases via the BLAST web pages (http://www.ncbi.nlm.nih.gov/BLAST/). All the algorithm-database combinations can be executed with default parameters or with customized settings, and the results can be viewed in a variety of ways. A new online resource, the BLAST Program Selection Guide, has been created to assist in the definition of search strategies. This article discusses optimal search strategies and highlights some BLAST features that can make your searches more powerful.

Figure 1

BLAST matches against the human genome presented in the NCBI Map Viewer. The query was the MEN1 mRNA (GenBank accession U93236) from (10). Ten alignments to NCBI RefSeq accession.version NT_033903.6 (a contig on chromosome 11) were found, corresponding to the 10 exons described in (10). The hits are marked as red or pink lines, depending upon the score (red indicates the strongest matches). The MEN1 exons are shown in blue, indicating a ‘Confirmed gene model’ (see http://www.ncbi.nlm.nih.gov/mapview/static/humansearch.html#genes for more information). The alignments are in reverse order owing to the antisense transcription on the genomic sequence (10).

Figure 2

A portion of the third table from the BLAST Program Selection Guide. The focus is on nucleotide queries. Starting from the left side the user chooses the proper row and then moves to the right. Assuming the user has a query >20 bases she would then have the choice between a nucleotide or protein database. For a nucleotide database the user should then pick a choice from the ‘purpose’ column that best describes her goal and use the corresponding link or links. Links from the BLAST Program column take you directly to the search page. The Learn More links provides a list of available databases.

Figure 3

The one-line descriptions in the BLAST report. The blue ‘L’ buttons on the right link to the LocusLink resource for each entry.

Figure 4

Query-anchored view of a query (Rab Escort Protein; Swiss-Prot accession P26374) against the human subset of nr. Only the first 60 residues of the P26374 alignment are shown. The top line of sequence represents the query; the other lines are the retrieved database sequences. The identifiers in the leftmost column correspond to the aligned sequence in that row; the numbers are NCBI GI numbers corresponding to the database sequences found. A ‘dot’ indicates an exact match between the query and database sequence; a letter indicates a substitution. The numbers represent the residue positions. For example, the fifth database sequence (NCBI GI number 624873) is aligned from residues 4–47. The first residue in this alignment is conserved (E), but the second is not (Y rather than F). The signatures of the motif—the bulky hydrophobic residues isoleucine (I), valine (V) and leucine (L)—are conserved, even if I is often switched for V, V for I and L for I. Only NCBI GI number 33352372 does not appear to contain this motif.