
                               primersearch 



Function

   Searches DNA sequences for matches with primer pairs

Description

   primersearch reads in primer pairs from an input file and searches
   them against sequence(s) specified by the user. Each of the primers in
   a pair is searched against the sequence and potential amplimers are
   reported.

   The user can specify a maximum percent mismatch level; for example,
   10% mismatch on a primer of length 20bp means that the program will
   classify a primer as matching a sequence if 18 of the 20 base pairs
   matches.

   It will only report matches if both primers in the pair have a match
   in opposite orientations.

Usage

   Here is a sample session with primersearch


% primersearch tembl:z52466 
Searches DNA sequences for matches with primer pairs
Primer file: primers
Allowed percent mismatch [0]: 
Output file [hsa203yc1.primersearch]: 

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

   Example 2

   Here we run the same example but allowing 20% mismatch between the
   primers and the sequence:


% primersearch tembl:z52466 
Searches DNA sequences for matches with primer pairs
Primer file: primers
Allowed percent mismatch [0]: 20
Output file [hsa203yc1.primersearch]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-seqall]            seqall     Sequence database USA
  [-primersfile]       infile     Primer file
  [-mismatchpercent]   integer    Allowed percent mismatch
  [-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
   -odirectory4         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
   [-primersfile]
   (Parameter 2) Primer file Input file Required
   [-mismatchpercent]
   (Parameter 3) Allowed percent mismatch Any integer value 0
   [-outfile]
   (Parameter 4) Output file name Output file <sequence>.primersearch
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   primersearch reads in any nucleic acid sequence USAs.

  Input files for usage example

   'tembl:z52466' is a sequence entry in the example nucleic acid
   database 'tembl'

  File: primers

# This is my primer file
D1S243  cacacaggctcacatgcc      gctccagcgtcatggact
D1S468 aattaaccgttttggtcct     gcgacacacacttccc
D1S2845 ccaaagggtgcttctc        gtggcattccaacctc
D1S1608 gatggcttttggggactatt    cactgagccaagtgacacag
D1S2893 aaaacatcaactctcccctg    ctcaaaccccaataagcctt
D1S2660 cacacatgcacatgcac       agtgacaccagcaggg

  Database entry: tembl:z52466

ID   HSA203YC1  standard; DNA; STS; 389 BP.
XX
AC   Z52466;
XX
SV   Z52466.1
XX
DT   18-MAR-1996 (Rel. 47, Created)
DT   23-MAR-1996 (Rel. 47, Last updated, Version 3)
XX
DE   H.sapiens (D1S2660) DNA segment containing (CA) repeat; clone AFMa203yc1;
DE   single read.
XX
KW   CA repeat; dinucleotide repeat; GT repeat; microsatellite DNA;
KW   microsatellite marker; repeat polymorphism; STS.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-389
RA   Weissenbach J.;
RT   ;
RL   Submitted (01-SEP-1995) to the EMBL/GenBank/DDBJ databases.
RL   Genethon, B.P. 60, 91002 Evry Cedex France. E-mail:
RL   Jean.Weissenbach@genethon.fr
XX
RN   [2]
RP   1-389
RX   MEDLINE; 96176476.
RA   Dib C., Faure S., Fizames C., Samson D., Drouot N., Vignal A.,
RA   Millasseau P., Marc S., Hazan J., Seboun E., Lathrop M., Gyapay G.,
RA   Morissette J., Weissenbach J.;
RT   "A comprehensive genetic map of the human genome based on 5,264
RT   microsatellites";
RL   Nature 380:152-154(1996).
XX
CC   full automatic;
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..389
FT                   /chromosome="1"
FT                   /db_xref="taxon:9606"
FT                   /note="cloning vector is M13mp18"
FT                   /organism="Homo sapiens"
FT                   /cell_line="CEPH 134702"
FT                   /clone_lib="genomic DNA"
XX
SQ   Sequence 389 BP; 118 A; 124 C; 86 G; 57 T; 4 other;
     agctgtgtgc acacaacatg anggggcaca catgcacatg cacacatgcc cacatgcata        6
0
     tgcacacaca cacacacaca cacacacaca ttcatgccca agcacgccca ccctcatgtc       12
0
     tcaccatgtg cacataacac acagtcacat ataccctggc acacatgccc acatgcagac       18
0
     acgaaacaca ggcccacgnt tncatgcaca caggtatggg cacacatacc atgcacacat       24
0
     aangacaaat accaggccag acatgatttg cccctgctgg tgtcactgtt aagtgtgaca       30
0
     gacaagcaga ggacacacac ccacctggga cgcggggctt caggagagag gcagacctaa       36
0
     tagggcccgg attcggggct ggggaggct                                         38
9
//

   The input primer file has the following format:

   Comment lines start with a '#'
   Lines with primer information have three fields separated by spaces or
   TAB characters. The columns contain:
    1. The name of the primer pair - this is reported in the output.
    2. The sequence of the first primer.
    3. The sequence of the second primer.

   Empty files will cause primersearch to note that no primers have been
   found, and to exit.

Output file format

  Output files for usage example

  File: hsa203yc1.primersearch


Primer name D1S243

Primer name D1S468

Primer name D1S2845

Primer name D1S1608

Primer name D1S2893

Primer name D1S2660
Amplimer 1
        Sequence: HSA203YC1 Z52466
        H.sapiens (D1S2660) DNA segment containing (CA) repeat; clone AFMa203yc
1; single read.
        CACACATGCACATGCAC hits forward strand at 27 with 0 mismatches
        AGTGACACCAGCAGGG hits reverse strand at [103] with 0 mismatches
        Amplimer length: 261 bp

  Output files for usage example 2

  File: hsa203yc1.primersearch


Primer name D1S243

Primer name D1S468

Primer name D1S2845

Primer name D1S1608

Primer name D1S2893

Primer name D1S2660
Amplimer 1
        Sequence: HSA203YC1 Z52466
        H.sapiens (D1S2660) DNA segment containing (CA) repeat; clone AFMa203yc
1; single read.
        CACACATGCACATGCAC hits forward strand at 49 with 2 mismatches
        AGTGACACCAGCAGGG hits reverse strand at [103] with 0 mismatches
        Amplimer length: 239 bp
Amplimer 2
        Sequence: HSA203YC1 Z52466
        H.sapiens (D1S2660) DNA segment containing (CA) repeat; clone AFMa203yc
1; single read.
        CACACATGCACATGCAC hits forward strand at 27 with 0 mismatches
        AGTGACACCAGCAGGG hits reverse strand at [103] with 0 mismatches
        Amplimer length: 261 bp

Data files

   None.

Notes

   Every potential amplimer will be reported; if one primer matches the
   forward strand twice and the other matches the reverse strand only
   once, two potential amplimers are reported. If the reverse primer
   matches twice, four potential amplimers are reported.

   Each primer pair consists of a name, followed by two primer sequences,
   primerA and primerB. The program first compares primerA to the forward
   strand and if it matches, primerB is compared to the reverse strand.
   The approach is then reversed, with the primerB being compared to the
   forward strand and primerA to the reverse. In this way all possible
   amplimers are reported.

References

   None.

Warnings

   This program is slow.
   Don't try searching all of EMBL!
   It might not be sensible to search all of the human section of EMBL -
   in 2000, this would take a day to do with one primer pair.
   It will take longer with more primer pairs.
   It will take longer if you allow mismatches.

Diagnostic Error Messages

   "No suitable primers found - exiting" means that either the primers
   file was empty or there were no compilable primer pairs contained in
   it.

Exit status

   It always exits with status 0

Known bugs

   None.

See also

   Program name Description
   eprimer3 Picks PCR primers and hybridization oligos
   stssearch Searches a DNA database for matches with a set of STS
   primers

   stssearch does something similar, but doesn't allow you to find
   mismatches and will report any match in any orientation and doesn't
   require you to have both primers matching.

Author(s)

   Val Curwen (vac © sanger.ac.uk)
   Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
   CB10 1SA, UK.

History

   Written Aug 2000 - Val Curwen

Target users

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

Comments

   None
