seqmatchall 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 All-against-all word comparison of a sequence set Description seqmatchall takes a set of sequences and does an all-against-all pairwise comparison of words of a specified size in the sequences, finding regions of identity between any two sequences. It writes an output file with a list of regions of identity in pairs of sequences, the start and end positions and length of the matching regions and the name of the sequences. Usage Here is a sample session with seqmatchall Here is an example using an increased word size to avoid accidental matches: % seqmatchall All-against-all word comparison of a sequence set Input sequence set: @eclac.list Word size [4]: 15 Output alignment [j01636.seqmatchall]: Go to the input files for this example Go to the output files for this example Command line arguments All-against-all word comparison of a sequence set Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqset Sequence set filename and optional format, or reference (input USA) -wordsize integer [4] Word size (Integer 2 or more) [-outfile] align [*.seqmatchall] Output alignment file name (default -aformat match) Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" 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 -aformat2 string Alignment format -aextension2 string File name extension -adirectory2 string Output directory -aname2 string Base file name -awidth2 integer Alignment width -aaccshow2 boolean Show accession number in the header -adesshow2 boolean Show description in the header -ausashow2 boolean Show the full USA in the alignment -aglobal2 boolean Show the full sequence in alignment 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 seqmatchall reads a set of nucleotide or protein sequences. The input is a standard EMBOSS sequence query (also known as a 'USA'). Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application. The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. 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 Output file format The output is a standard EMBOSS alignment file. The results can be output in one of several styles by using the command-line qualifier -aformat xxx, where 'xxx' is replaced by the name of the required format. Some of the alignment formats can cope with an unlimited number of sequences, while others are only for pairs of sequences. The available multiple alignment format names are: multiple, simple, fasta, msf, clustal, mega, meganon, nexus,, nexusnon, phylip, phylipnon, selex, treecon, tcoffee, debug, srs. The available pairwise alignment format names are: pair, markx0, markx1, markx2, markx3, markx10, match, sam, bam, score, srspair See: http://emboss.sf.net/docs/themes/AlignFormats.html for further information on alignment formats. By default the output is in 'match' format. Output files for usage example File: j01636.seqmatchall ######################################## # Program: seqmatchall # Rundate: Fri 15 Jul 2011 12:00:00 # Commandline: seqmatchall # -sequence @../../data/eclac.list # -wordsize 15 # Align_format: match # Report_file: j01636.seqmatchall ######################################## #======================================= # # Aligned_sequences: 2 # 1: J01636 # 2: X51872 #======================================= 1832 J01636 + 5646..7477 X51872 + 1..1832 #======================================= # # Aligned_sequences: 2 # 1: J01636 # 2: V00294 #======================================= 1113 J01636 + 49..1161 V00294 + 1..1113 #======================================= # # Aligned_sequences: 2 # 1: J01636 # 2: V00295 #======================================= 1500 J01636 + 4305..5804 V00295 + 1..1500 #======================================= # # Aligned_sequences: 2 # 1: J01636 # 2: V00296 #======================================= 3078 J01636 + 1287..4364 V00296 + 1..3078 #======================================= # # Aligned_sequences: 2 # 1: X51872 # 2: V00295 #======================================= 159 X51872 + 1..159 V00295 + 1342..1500 #======================================= # # Aligned_sequences: 2 # 1: V00295 # 2: V00296 #======================================= 60 V00295 + 1..60 V00296 + 3019..3078 #--------------------------------------- #--------------------------------------- J01636 (the complete E.coli lac operon) matches V00294 V00295 V00296 and X51872 (the individual genes), and there is a short overlap between V00295 (lacY) and the flanking genes V00296 (lacZ) and X51872 (lacA) The output is a list of regions of identity in pairs of sequences, each consisting of one line with 7 columns of data separated by TABs or space characters. The columns of data consist of: * The length of the region of identity. * The start position in sequence 1. * The end position in sequence 1. * The name of sequence 1. * The start position in sequence 2. * The end position in sequence 2. * The name of sequence 2. Data files None. Notes The larger the specified word size, the faster the comparison will proceed. Regions whose stretches of identity are shorter than the word size will be missed. You should therefore choose a word size that is small enough to find those regions of similarity you are interested in within a reasonable time-frame. References None. Warnings None. Diagnostic Error Messages None. Exit status It exits with a status of 0. Known bugs None. See also Program name Description matcher Waterman-Eggert local alignment of two sequences supermatcher Calculate approximate local pair-wise alignments of larger sequences water Smith-Waterman local alignment of sequences wordfinder Match large sequences against one or more other sequences wordmatch Finds regions of identity (exact matches) of two sequences polydot will give a graphical view of the same matches. Author(s) Ian Longden formerly at: Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History 1999 - written - Ian Longden Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None