StsSearch looks for primer pairs in a set of sequences.
StsSearch compares a list of primer pairs to a set of sequences, and reports any sequences in which both primers are found exactly, and in the correct orientation.
This program was written by Peter Rice (E-mail: email@example.com Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).
All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (firstname.lastname@example.org).
Here is a sample session with StsSearch The sts.primers file can be copied to your directory by the command "fetch egenrundata:sts.primers".
% stssearch STSSEARCH uses nucleotide sequences STSSEARCH of what sequence(s) ? Em_Sts:Bt* What file ? sts.primers What should I call the output file (* bt15431.sts *) ? bt.sts What should I call the error file (* bt.err *) ? Primers: 4 Entries: 178 Bases: 69,751 CPU Time: 7.460000 %
The output from StsSearch is a simple report of hits in the sequence. The error file reports near misses, for example where only one primer of a pair hits in a sequence.
EM_STS:BT15433 + 106 RME23f 76 RME23r 181 EM_STS:BT15434 + 94 RME25f 116 RME25r 209
The input file for StsSearch contains an optional heading (ending with a line containing ".."), and pairs of sequences, one per line with a name, as in the example below:
Examples for the STSSEARCH program. Primers taken from two Bos taurus entries in the em_sts division so they can be searched against em_sts:bt* which at present (mid 1995) is not too many .. RME23 GTGAGTACAGGCGCTTTCTG AGAACAAATGTGACACTCACA RME25 TTAAAGATCCCAGCCTGTGC AGTGGGTAAAGGAGCCTGGT
All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.
Minimum Syntax: % stssearch [-INfile1=]Em_Sts:Hs* [-INfile2=]sts.primers -Default Prompted Parameters: [-OUTfile=]results.sts Output file [-ERRfile=]results.err Error message file Optional Parameters: -NOSUMmary Do not write summary statistics at end of run -PRIMer1=cagtcgtcgta Sequence of forward primer -PRIMer2=ttctagcagta Sequence of reverse primer -NAme1=PrimerA Name of forward primer -NAme2=PrimerB Name of reverse primer
The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.
Description of the option in a few lines
Do not write summary statistics at end of run.
Sequence of a single forward primer instead of a list file. If used, both primer1 and primer2 must be provided.
Sequence of a single reverse primer instead of a list file. If used, both primer1 and primer2 must be provided.
Name of forward primer when these are on the command line.
Name of reverse primer when these are on the command line.
Printed: April 22, 1996 15:55 (1162)