This command performs the Gap4 "Suggest Probes" function. It searches for
unique sequences at the ends of contigs suitable for probing clone
libraries to pick overlapping sequences and hence to extend contigs. The
command returns a newline separated list of probes in the form
The database IO handle returned from a previous
This specifies the list of contigs to use. Only the contig identifier is
currently used, although the syntax specifying start and end ranges is valid.
These specify an inclusive range of the allowed lengths of probes chosen.
The defaults are min_size of 15 and max_size of 19.
Each potential probe sequence is comparared against all contig sequences
and, optionally, several vector sequences. This option specifies the
maximum percentage match between the probe and the comparison sequences.
Only sequences with no matches above this percentage match are considered
unique. sequences. The default is 90.0.
These specify the area in which to look for probes as an offset from the
ends of the contigs. The defaults are from 10 to 100.
This specifies a file of vector filenames. NB: This will possibly be changed
to a Tcl list of vector filenames. The uniqueness search will then also check
the vector files for matches. The vector files can be in any format readable
by the seq_utils library (currently Staden, EMBL, CODATA, GENBANK and
FASTA). The default is blank, which implies no vectors to check.
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Last generated on 1 March 2001.