There have been three main improvements to the NCBI BLAST web site this year. The first is the addition of Sequence Read Archive (SRA) transcript libraries as a new search set, which includes all public sequences from 454 sequencing systems. These sequences can be searched using the ‘Search SRA transcript libraries’ link in the ‘Specialized BLAST’ section of the BLAST web site. NCBI has also reorganized the page for aligning two sequences using BLAST (bl2seq), which now has a search page consistent with the other BLAST pages. On this page, users can enter multiple query sequences and multiple subject sequences, instead of one each as on the older page. The report for the new page is also a standard BLAST report, although a ‘Dot Matrix View’ is available if only one query and one subject sequence are entered. Finally, the BLASTP report now offers a new ‘Multiple Alignment’ option that uses COBALT (6) to perform a multiple alignment of the query sequence and any subject sequences listed in the BLAST report. If the user selects this link, a separate multiple alignment search is started and displayed in a separate browser window.
