CSC

find_oligo

find_oligo
 -io            io_handle:integer
 -contigs       identifiers:strings
?-min_pmatch    percentage:float(75.0)?
?-seq           sequence:string()?
?-tag_types     types:string()?

This command searches for short sequence segments and plots them in the Contig Selector. It will fail when not running in a graphical environment containing the Contig Selector. The function returns no value but will generate a Tcl error if an error occurs.

-io io_handle

The database IO handle returned from a previous open_db call.

-contigs identifiers

This specifies the list of contigs to search. The {contig start end} syntax may be used for an identifier to search only a region of the contig, otherwise all of it is searched.

-min_pmatch percentage

Only matches with this level of similarity or better will be displayed. The default is 75%.

-seq sequence

The command will search for the sequence in each of the specified contigs, plotting matches above (or equal to) the mininum percentage match. This option takes precedence over the -tag_types option. The default is a blank string, which implies no searching.

-tag_types types

If a list of tag types is specified the algorithm first obtains the sequence underneath each tag of these types. For each sequence the search is independently performed with that sequence as the search string. If -seq has also been specified this option is invalid. The default is a blank list of tag types, which implies no tags will be searched for.