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