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
(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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Last generated on 22 October 2002.