The NCBI BLAST web pages (blastn, blastp, blastx, tblastn, tblastx ) have a new option to align a query against a set of target sequences, rather than a BLAST database.This option allows you to align your query to one or more subject sequences and still use the standard BLAST web interface to optimize your search and change algorithm parameters. Each search is assigned a "Request ID" (RID) and is also listed under the "Recent Results" tab that you can access from the BLAST home page at http://blast.ncbi.nlm.nih.gov/Blast.cgi. The results are formatted as a standard BLAST report, except a "Dot Matrix view" (a "dot-plot" like graphic of the alignments) is available in the new report design if only one subject sequence was searched. Step-by-step instructions can be found at http://blast.ncbi.nlm.nih.gov/docs/align_seqs.pdf
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