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seqmatchall |
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.
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
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
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. 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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required |
| -wordsize | Word size | Integer 2 or more | 4 |
| [-outfile] (Parameter 2) |
Output alignment file name | Alignment output file | <*>.seqmatchall |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
The sequences must be either all protein or all nucleic acid.
#Formerly ECLAC tembl:J01636 #Formerly ECLACA tembl:X51872 #Formerly ECLACI tembl:V00294 #Formerly ECLACY tembl:V00295 #Formerly ECLACZ tembl:V00296 |
########################################
# Program: seqmatchall
# Rundate: Tue 15 Jul 2008 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 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.
| 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.