stssearch Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Search a DNA database for matches with a set of STS primers Description stssearch searches one or more DNA sequences with a set of STS primers and reports expected matches. The database to search, the input primer pairs file and an output file for matches are specified. For each pair of primers, it looks for matches between the primers and the query sequence in either orientation. Details of any matches are written to the output file. 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 nucleotide sequence(s): @eclac.list Primer pairs file: lac.primers Output file [j01636.stssearch]: Go to the input files for this example Go to the output files for this example Command line arguments Search a DNA database for matches with a set of STS primers Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-seqall] seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) [-infile] infile Primer pairs file [-outfile] outfile [*.stssearch] 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 first file to standard output -filter boolean Read first file from standard input, write first file to 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 and exit. 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 dying program messages -version boolean Report version number and exit Input file format Input files for usage example File: eclac.list #Formerly ECLAC tembl:J01636 #Formerly ECLACA tembl:X51872 #Formerly ECLACI tembl:V00294 #Formerly ECLACY tembl:V00295 #Formerly ECLACZ tembl:V00296 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: j01636.stssearch J01636: PrimA PrimerA matched at 532 J01636: (rev) PrimA PrimerB matched at 689 J01636: PrimB PrimerA matched at 5743 J01636: (rev) PrimB PrimerB matched at 5942 J01636: PrimC PrimerA matched at 2954 J01636: (rev) PrimC PrimerB matched at 3069 J01636: PrimD PrimerA matched at 1074 J01636: (rev) PrimD PrimerB matched at 1261 J01636: PrimE PrimerA matched at 1074 X51872: PrimB PrimerA matched at 98 X51872: (rev) PrimB PrimerB matched at 297 V00294: PrimA PrimerA matched at 484 V00294: (rev) PrimA PrimerB matched at 641 V00294: PrimD PrimerA matched at 1026 V00294: PrimE PrimerA matched at 1026 V00295: PrimB PrimerA matched at 1439 V00296: PrimC PrimerA matched at 1668 V00296: (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 eprimer32 Picks PCR primers and hybridization oligos primersearch Search 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 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None