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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:6.6.0.0
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
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-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: Mon 15 Jul 2013 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 Find 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
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