| ## EMBOSS: stssearch

# Program stssearch

## Function

Searches a DNA database for matches with a set of STS primers

## Description

Searches a DNA sequence database with a set of STS primers and reports expected matches and possible mismatches. A replacement for stssearch in the EGCG package.

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

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

## Usage

Here is a sample session with stssearch.

    % stssearch
    Input sequence(s): embl:eclac*
    Primer file: lac.primers

## Command line arguments

       Mandatory qualifiers:
      [-sequences]         seqall     Sequence database USA
      [-primers]           infile     Primer file
      [-out]               outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequences] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-primers] (Parameter 2) | Primer file | Input file | Required
[-out] (Parameter 3) | Output file name | Output file | <sequence>.stssearch
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Here is the primer input file for the example run:

    PrimA ACCAGACACCCATCAACAG    TATTTATGCCAGCCAGCCAG
    PrimB CGAAAGAATAAGAGCAGGCAAG GTAAGAGAAATAGACAGGCGG
    PrimC CGTCAGTATCCCCGTTTACAG  TATCGCCAAAATCACCGCC
    PrimD AATACGCAAACCGCCTCTCC   TTATCCGCTCACAATTCCACAC
    PrimE AATACGCAAACCGCCTCTCC   CACAACCCGCTCACAATTCCA

It 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

Here is the output from the example run:

    ECLAC: PrimA PrimerA matched at 532
    ECLAC: (rev) PrimA PrimerB matched at 689
    ECLAC: PrimB PrimerA matched at 5743
    ECLAC: (rev) PrimB PrimerB matched at 5942
    ECLAC: PrimC PrimerA matched at 2954
    ECLAC: (rev) PrimC PrimerB matched at 3069
    ECLAC: PrimD PrimerA matched at 1074
    ECLAC: (rev) PrimD PrimerB matched at 1261
    ECLAC: PrimE PrimerA matched at 1074
    ECLACA: PrimB PrimerA matched at 98
    ECLACA: (rev) PrimB PrimerB matched at 297
    ECLACI: PrimA PrimerA matched at 484
    ECLACI: (rev) PrimA PrimerB matched at 641
    ECLACI: PrimD PrimerA matched at 1026
    ECLACI: PrimE PrimerA matched at 1026
    ECLACY: PrimB PrimerA matched at 1439
    ECLACZ: PrimC PrimerA matched at 1668
    ECLACZ: (rev) PrimC PrimerB matched at 1783

This consists of one line per match. This consists of:

- The name of the sequence that the match is found in, followed by a ':'.
- If the match is in the reverse sense, it has a '(rev)'.
- The name of the primer pair.
- 'PrimerA' or 'PrimerB'.
- 'matched at' the start of the match position.

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

None.

## Known bugs

None.

## See also

Program name | Description
--- | ---
eprimer3 | Picks PCR primers and hybridization oligos
primersearch | Searches DNA sequences for matches with primer pairs

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

## Author(s)

This application was written by Peter Rice (pmr@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## History

Finished.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments