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.

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

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

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

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

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

Target users

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

Comments