first previous next last contents

Screen Sequences

Filename
screen_seq.p4m

Description
This module can perform very fast matches between the sequences to process and one or more screen sequences. Any sequence containing a significant match is rejected. An example of use for this module is to reject sequences prior to assembly that appear to be contaminated with E.Coli. This uses the screen_seq program (see section Screen_seq).

Option: Screen single sequence
This is yes/no question used to determine whether the screen sequence filename is the filename of a single sequence or a filename of a file containing a series of sequence filenames. To compare just one file select "Yes".

Option: Screen sequence file (of filenames)
This is either the filename of a single sequence or the filename of a file of filenames, depending on the answer to the previous question. The sequence files must be in plain text format containing just the bases or white space.

Option: Maximum screen sequence length
The maximum length of any individual screen sequence.

Option: Minimum match length
Any fragment containing an exact match longer than this length will be rejected.


first previous next last contents
This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_20.html