find_probes

find_probes
 -io            io_handle:integer
 -contigs       identifiers:strings
?-min_size      length:integer(15)?
?-max_size      length:integer(19)?
?-max_pmatch    fraction:float(90.0)?
?-from          position:integer(10)?
?-to            position:integer(100)?
?-vectors       filename:string()?

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 "Contig ident position int Tm int sequence string".

-io io_handle

The database IO handle returned from a previous open_db call.

-contigs identifiers

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.

-min_size length

-max_size length

These specify an inclusive range of the allowed lengths of probes chosen. The defaults are min_size of 15 and max_size of 19.

-max_pmatch fraction

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.

-from position

-to position

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.

-vectors filename

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.