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seqmatchall |
Wiki
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Function
All-against-all word comparison of a sequence setDescription
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 seqmatchallHere 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
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
seqset | Sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required |
| -wordsize | integer | Word size | Integer 2 or more | 4 |
| [-outfile] (Parameter 2) |
align | Output alignment file name | (default -aformat match) | <*>.seqmatchall |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated seqset qualifiers | ||||
| -sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |
| -sid1 -sid_sequence |
string | Entryname | Any string | |
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |
| -fformat1 -fformat_sequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
| "-outfile" associated align qualifiers | ||||
| -aformat2 -aformat_outfile |
string | Alignment format | Any string | match |
| -aextension2 -aextension_outfile |
string | File name extension | Any string | |
| -adirectory2 -adirectory_outfile |
string | Output directory | Any string | |
| -aname2 -aname_outfile |
string | Base file name | Any string | |
| -awidth2 -awidth_outfile |
integer | Alignment width | Any integer value | 0 |
| -aaccshow2 -aaccshow_outfile |
boolean | Show accession number in the header | Boolean value Yes/No | N |
| -adesshow2 -adesshow_outfile |
boolean | Show description in the header | Boolean value Yes/No | N |
| -ausashow2 -ausashow_outfile |
boolean | Show the full USA in the alignment | Boolean value Yes/No | N |
| -aglobal2 -aglobal_outfile |
boolean | Show the full sequence in alignment | Boolean value Yes/No | N |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
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
#---------------------------------------
#---------------------------------------
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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 © emboss.open-bio.org) not to the original author.