
                                 stssearch 



Function

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

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

   Here is a sample session with stssearch


% stssearch 
Search a DNA database for matches with a set of STS primers
Input sequence(s): tembl:eclac*
Primer file: lac.primers
Output file [eclac.stssearch]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-seqall]            seqall     Sequence database USA
  [-infile]            infile     Primer file
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-seqall" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory3        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-seqall]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-infile]
   (Parameter 2) Primer file Input file Required
   [-outfile]
   (Parameter 3) Output file name Output file <sequence>.stssearch
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

  Input files for usage example

   'tembl:eclac*' is a sequence entry in the example nucleic acid
   database 'tembl'

  File: lac.primers

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

   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

  Output files for usage example

  File: eclac.stssearch

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

   The output file 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)

   Peter Rice (pmr © ebi.ac.uk)
   Informatics Division, European Bioinformatics Institute, Wellcome
   Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

Target users

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

Comments

   None
