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VECTORSTRIP application details page
Strips out DNA between a pair of vector sequences
vectorstrip is intended to be useful for stripping vector sequencefrom the ends of sequences of interest. For example, if a fragment hasbeen cloned into a vector and then sequenced, the sequence may containvector data eg from the cloning polylinker at the 5' and 3' ends ofthe sequence. vectorstrip will remove these contaminating regions andoutput trimmed sequence ready for input into another application. vectorstrip is suitable for use with low quality sequence data as itcan allow for mismatches between the sequence and the vector patternsprovided. You can specify the maximum level of mismatchexpected. Vector data can either be provided in a file or interactively. Ifpresented in a file, vectorstrip will search all input sequences withall vectors listed in that file. The intention is that the user canmaintain a single file for use with vectorstrip, containing all thelinker sequences commonly used in the laboratory. The two patterns for each vector are searched separately against thesequence. Once the search is completed, each of the hits of the 5'sequence is paired with each of the hits of the 3' sequence and theresulting subsequences are output. For example, if the 5' sequencematches the sequence from (a) position 30-60, and(b)position 70-100,and the 3' sequence matches from 150-175, then two subsequences willbe output: from 61-149, and from 101-149. The lower the quality ofthe sequence, the more likely multiple hits become if nonzeromismatches are accepted. Default behaviour is to report only the best matches between thevector patterns and the sequence. This means that if youspecify a maximum mismatch level of 10%, but the vector patternsmatch the sequence with zero mismatches, the search will stop and theprogram will output only these "best" matches. If there are no perfectmatches, the program will try searching again allowing 1 mismatch,then 2, and so on until either the patterns match the sequence or themaximum specified mismatch level is exceeded. You can tell vectorstripto show all possible matches up to your specified maximum level, asillustrated in the examples below.
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