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Cross_match

Filename
cross_match_svec.p4m

Description
This uses the cross_match program to search for sequencing vector. (Future versions may also check for other cloning vectors.) This allows for searching of multiple vector files. However as cross_match does not make use of primer and cut site information the vector detection is inherently less sensitive than vector_clip (see section Screening against Vector Sequences). Cross_match is not included as part of the Staden Package. It is available from Phil Green. Green, P. http://www.genome.washington.edu/UWGC/analysistools/swat.htm.

Option: FASTA vector file name
This specifies a fasta format file of one or more sequencing vector sequences.

Option: Minimum match length
Minimum length of matching word for SWAT comparison.

Option: Minimum score
Minimum SWAT score.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_16.html