Cross_match

Cross_match is not included as part of the Staden Package. It is available from Phil Green. http://www.genome.washington.edu/UWGC/analysistools/swat.htm

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).

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.