Old Cloning Vector Clip - Obsolete

Description

This is an older version of the Cloning Vector Clip module. It still uses the vector_clip program to perform this task, but does not use the newer probabilistic model for analysing matches. It is still present as an option for people who have tuned the parameters for their data and are happy with this. The probability mode is recommended (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: Word length

Option: Number of diagonals

Option: Diagonal score

The searching method involves hashing words to quickly identify matches and then combining these words along the best and neighbouring diagonals to produce an overall score which is compared against the diagonal score to determine whether this is vector sequence. The score is normalised from 0 (no match) to 1.0 (perfect match). For full details on this see the vector_clip manual.