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Screen Sequences


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.

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.