BLAST: improvements for better sequence analysis

Abstract

Basic local alignment search tool (BLAST) is a sequence similarity search program. The National Center for Biotechnology Information (NCBI) maintains a BLAST server with a home page at http://www.ncbi.nlm.nih.gov/BLAST/. We report here on recent enhancements to the results produced by the BLAST server at the NCBI. These include features to highlight mismatches between similar sequences, show where the query was masked for low-complexity sequence, and integrate information about the database sequences from the NCBI Entrez system into the BLAST display. Changes to how the database sequences are fetched have also improved the speed of the report generator.

Figure 1

Excerpt from a BLAST result showing custom-definition lines. The query was bases 241 through 480 of a human MHC A gene nucleotide sequence (NM_002116) in a search against the human genome. The top line of the figure is the traditional sequence definition. Custom definition lines are provided for both of the alignments shown and are relevant to the region matched (first alignment) or nearby regions (second alignment).

Figure 2

Demonstration of new format options. FASTA sequence for the human cystic fibrosis trans-membrane conductance regulator sequence (NM_000492) was used as query for a BLASTN search against the nr database using default parameters. Three new display options are shown in this figure. The first is the ‘Pairwise with identities’ option. Nucleotide matches in the database sequence are shown as dots (‘.’), nucleotide mismatches in the database sequence (as well as the database sequence identification) are colored red. The second new option is the presentation of the CDS features, which is shown for both the query and database sequences above and below the BLAST alignment, respectively. The CDS feature annotated on the database sequence was retrieved from Entrez; the putative CDS feature on the query was produced automatically using the CDS of the database sequence as a guide. Mismatches for the amino acid sequence derived from the database sequence are colored pink. Finally the new masking option is shown (see text). Bases 175–181 of the query were masked for low-complexity during the search and are shown in lower-case gray letters.

Figure 3

Enabling new features on the BLAST format page. The red arrows point to new report features that may be enabled or modified from this page. The check-box highlighted by arrow 1 enables the CDS feature on a BLASTN or megaBLAST search. The two menus highlighted by arrow 2 change the default behavior for display of masked regions. The menu highlighted by arrow 3 changes how the alignments are displayed in the BLAST report.