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)

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:

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

None.

Known bugs

None.

See also

Program nameDescription
dotmatcherDisplays a thresholded dotplot of two sequences
polydotDisplays all-against-all dotplots of a set of sequences
primaSelects primers for PCR and DNA amplification
primersearchSearches DNA sequences for matches with primer pairs
seqmatchallDoes an all-against-all comparison of a set of sequences
supermatcherFinds a match of a large sequence against one or more sequences
wordmatchFinds all exact matches of a given size between 2 sequences

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