April 15, 2012 (Vol. 32, No. 8)
Strong Points: Large database, nice sequence alignments and phylogenetic trees
Weak Points: Users cannot alter search stringency parameters
Vectors (plasmids, cosmids, BACs, etc.) are certainly friends to the researcher—we all use these valuable DNA constructs to clone and manipulate our DNA sequences of interest. But, what happens when (dun, dun, DUN!) vectors turn against us?! OK, so it’s not quite that dramatic, but it is true that vector contamination is a legitimate threat when it comes to sequencing your precious DNA of interest. So how can you be sure that a particular DNA sequence—be it your own or one that you found online—is free from contamination? The NCBI actually offers an online resource for exactly that purpose. VecScreen allows users to input a query sequence (via Accession number, GI, or FASTA sequence) and search it against an extensive database of vector sequences. The search tool subsequently identifies fragments that may be of vector origin.