stssearch

Function

Description

stssearch searches a DNA sequence database with a set of STS primers and reports expected matches.

stssearchs reads in one or more sequences to be searched. For each pair of primers, it looks for matches between a the primers and the query sequence in either orientation.

Any matches found will be reported. Only one primer need match for it to be reported..

Usage

Command line arguments


Input file format

The primers file consists of three columns separated by tabs or spaces.

The first column is the name of the primer pair.
The second column is the sequence of the first primer.
The third column is the sequence of the second primer.

Output file format

The output file consists of one line per match. This consists of:

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

None.

Known bugs

None.

If you want something that only reports matches of both primer pairs and can find mismatches, use primersearch.

Author(s)

History

Target users

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