seqmatchall

 

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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:6.5.0.0

   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
   -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

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
-scircular1
-scircular_sequence
boolean Sequence is circular Boolean value Yes/No N
-sformat1
-sformat_sequence
string Input sequence format Any string  
-iquery1
-iquery_sequence
string Input query fields or ID list Any string  
-ioffset1
-ioffset_sequence
integer Input start position offset Any integer value 0
-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: Sun 15 Jul 2012 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:

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 © 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