Cloning Vector Clip

Filename

cloning_vector_clip.p4m

Description

This module searches for non "sequencing" vectors used in the shotgunning process, eg for Cosmid or YAC. Any fragment in any orientation of this vector could be present so there is no need for the cut sites to be known. The vector_clip program is used for this task (see section Screening against Vector Sequences).

Option: Vector file name

The filename containing the vector sequence. At present this should be a file containing a single plain text sequence containing just the bases or white space.

Option: Max probability

This option specifies the maximum probability of a particular match occurring by chance. Any match found with lower than this probability will be assumed to be real match, hence lower values represent more stringent matching.