Tehdyt toimenpiteet
|
matcher |
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
Waterman-Eggert local alignment of two sequencesDescription
matcher identifies local similarities in two input sequences using a rigorous algorithm based on Bill Pearson's lalign application, version 2.0u4 (Feb. 1996). The substitution matrix, gap insertion and extension penalty are specified. The specified number of top-scoring pair-wise local sequence alignments are written to file.
Algorithm
matcher is based on Bill Pearson's lalign application, version 2.0u4 (Feb. 1996). lalign uses code developed by X. Huang and W. Miller (Adv. Appl. Math. (1991) 12:337-357) for the "sim" program, which is a linear-space version of an algorithm described by M. S. Waterman and M. Eggert (J. Mol. Biol. 197:723-728).
Usage
Here is a sample session with matcher
% matcher tsw:hba_human tsw:hbb_human Waterman-Eggert local alignment of two sequences Output alignment [hba_human.matcher]: |
Go to the input files for this example
Go to the output files for this example
Example 2
To find the 10 best alignments:
% matcher tsw:hba_human tsw:hbb_human -alt 10 Waterman-Eggert local alignment of two sequences Output alignment [hba_human.matcher]: |
Go to the output files for this example
Command line arguments
Waterman-Eggert local alignment of two sequences
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-asequence] sequence Sequence filename and optional format, or
reference (input USA)
[-bsequence] sequence Sequence filename and optional format, or
reference (input USA)
[-outfile] align [*.matcher] Output alignment file name
(default -aformat markx0)
Additional (Optional) qualifiers:
-datafile matrix [EBLOSUM62 for protein, EDNAFULL for DNA]
This is the scoring matrix file used when
comparing sequences. By default it is the
file 'EBLOSUM62' (for proteins) or the file
'EDNAFULL' (for nucleic sequences). These
files are found in the 'data' directory of
the EMBOSS installation.
-alternatives integer [1] This sets the number of alternative
matches output. By default only the highest
scoring alignment is shown. A value of 2
gives you other reasonable alignments. In
some cases, for example multidomain proteins
of cDNA and genomic DNA comparisons, there
may be other interesting and significant
alignments. (Integer 1 or more)
-gapopen integer [14 for protein, 16 for nucleic] The gap
penalty is the score taken away when a gap
is created. The best value depends on the
choice of comparison matrix. The default
value of 14 assumes you are using the
EBLOSUM62 matrix for protein sequences, or a
value of 16 and the EDNAFULL matrix for
nucleotide sequences. (Positive integer)
-gapextend integer [4 for any sequence] The gap length, or gap
extension, penalty is added to the standard
gap penalty for each base or residue in the
gap. This is how long gaps are penalized.
Usually you will expect a few long gaps
rather than many short gaps, so the gap
extension penalty should be lower than the
gap penalty. An exception is where one or
both sequences are single reads with
possible sequencing errors in which case you
would expect many single base gaps. You can
get this result by setting the gap penalty
to zero (or very low) and using the gap
extension penalty to control gap scoring.
(Positive integer)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-asequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the 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
"-bsequence" associated qualifiers
-sbegin2 integer Start of the sequence to be used
-send2 integer End of the sequence to be used
-sreverse2 boolean Reverse (if DNA)
-sask2 boolean Ask for begin/end/reverse
-snucleotide2 boolean Sequence is nucleotide
-sprotein2 boolean Sequence is protein
-slower2 boolean Make lower case
-supper2 boolean Make upper case
-sformat2 string Input sequence format
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 string Features file name
"-outfile" associated qualifiers
-aformat3 string Alignment format
-aextension3 string File name extension
-adirectory3 string Output directory
-aname3 string Base file name
-awidth3 integer Alignment width
-aaccshow3 boolean Show accession number in the header
-adesshow3 boolean Show description in the header
-ausashow3 boolean Show the full USA in the alignment
-aglobal3 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 | ||||
| [-asequence] (Parameter 1) |
sequence | Sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| [-bsequence] (Parameter 2) |
sequence | Sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| [-outfile] (Parameter 3) |
align | Output alignment file name | (default -aformat markx0) | <*>.matcher |
| Additional (Optional) qualifiers | ||||
| -datafile | matrix | This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA |
| -alternatives | integer | This sets the number of alternative matches output. By default only the highest scoring alignment is shown. A value of 2 gives you other reasonable alignments. In some cases, for example multidomain proteins of cDNA and genomic DNA comparisons, there may be other interesting and significant alignments. | Integer 1 or more | 1 |
| -gapopen | integer | The gap penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value of 14 assumes you are using the EBLOSUM62 matrix for protein sequences, or a value of 16 and the EDNAFULL matrix for nucleotide sequences. | Positive integer | 14 for protein, 16 for nucleic |
| -gapextend | integer | The gap length, or gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap penalty to zero (or very low) and using the gap extension penalty to control gap scoring. | Positive integer | 4 for any sequence |
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-asequence" associated sequence qualifiers | ||||
| -sbegin1 -sbegin_asequence |
integer | Start of the sequence to be used | Any integer value | 0 |
| -send1 -send_asequence |
integer | End of the sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_asequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_asequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_asequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_asequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_asequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_asequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_asequence |
string | Input sequence format | Any string | |
| -sdbname1 -sdbname_asequence |
string | Database name | Any string | |
| -sid1 -sid_asequence |
string | Entryname | Any string | |
| -ufo1 -ufo_asequence |
string | UFO features | Any string | |
| -fformat1 -fformat_asequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_asequence |
string | Features file name | Any string | |
| "-bsequence" associated sequence qualifiers | ||||
| -sbegin2 -sbegin_bsequence |
integer | Start of the sequence to be used | Any integer value | 0 |
| -send2 -send_bsequence |
integer | End of the sequence to be used | Any integer value | 0 |
| -sreverse2 -sreverse_bsequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask2 -sask_bsequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide2 -snucleotide_bsequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein2 -sprotein_bsequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower2 -slower_bsequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper2 -supper_bsequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat2 -sformat_bsequence |
string | Input sequence format | Any string | |
| -sdbname2 -sdbname_bsequence |
string | Database name | Any string | |
| -sid2 -sid_bsequence |
string | Entryname | Any string | |
| -ufo2 -ufo_bsequence |
string | UFO features | Any string | |
| -fformat2 -fformat_bsequence |
string | Features format | Any string | |
| -fopenfile2 -fopenfile_bsequence |
string | Features file name | Any string | |
| "-outfile" associated align qualifiers | ||||
| -aformat3 -aformat_outfile |
string | Alignment format | Any string | markx0 |
| -aextension3 -aextension_outfile |
string | File name extension | Any string | |
| -adirectory3 -adirectory_outfile |
string | Output directory | Any string | |
| -aname3 -aname_outfile |
string | Base file name | Any string | |
| -awidth3 -awidth_outfile |
integer | Alignment width | Any integer value | 0 |
| -aaccshow3 -aaccshow_outfile |
boolean | Show accession number in the header | Boolean value Yes/No | N |
| -adesshow3 -adesshow_outfile |
boolean | Show description in the header | Boolean value Yes/No | N |
| -ausashow3 -ausashow_outfile |
boolean | Show the full USA in the alignment | Boolean value Yes/No | N |
| -aglobal3 -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
matcher reads in two 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
'tsw:hba_human' is a sequence entry in the example protein database 'tsw'
Database entry: tsw:hba_human
ID HBA_HUMAN Reviewed; 142 AA.
AC P69905; P01922; Q1HDT5; Q3MIF5; Q53F97; Q96KF1; Q9NYR7; Q9UCM0;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 15-JUN-2010, entry version 86.
DE RecName: Full=Hemoglobin subunit alpha;
DE AltName: Full=Hemoglobin alpha chain;
DE AltName: Full=Alpha-globin;
GN Name=HBA1;
GN and
GN Name=HBA2;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HBA1).
RX MEDLINE=81088339; PubMed=7448866; DOI=10.1016/0092-8674(80)90347-5;
RA Michelson A.M., Orkin S.H.;
RT "The 3' untranslated regions of the duplicated human alpha-globin
RT genes are unexpectedly divergent.";
RL Cell 22:371-377(1980).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (HBA2).
RX MEDLINE=80137531; PubMed=6244294;
RA Wilson J.T., Wilson L.B., Reddy V.B., Cavallesco C., Ghosh P.K.,
RA Deriel J.K., Forget B.G., Weissman S.M.;
RT "Nucleotide sequence of the coding portion of human alpha globin
RT messenger RNA.";
RL J. Biol. Chem. 255:2807-2815(1980).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HBA2).
RX MEDLINE=81175088; PubMed=6452630; DOI=10.1073/pnas.77.12.7054;
RA Liebhaber S.A., Goossens M.J., Kan Y.W.;
RT "Cloning and complete nucleotide sequence of human 5'-alpha-globin
RT gene.";
RL Proc. Natl. Acad. Sci. U.S.A. 77:7054-7058(1980).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6946451; DOI=10.1073/pnas.78.8.5041;
RA Orkin S.H., Goff S.C., Hechtman R.L.;
RT "Mutation in an intervening sequence splice junction in man.";
RL Proc. Natl. Acad. Sci. U.S.A. 78:5041-5045(1981).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT LYS-32.
RX MEDLINE=21303311; PubMed=11410421;
RA Zhao Y., Xu X.;
RT "Alpha2(CD31 AGG-->AAG, Arg-->Lys) causing non-deletional alpha-
RT thalassemia in a Chinese family with HbH disease.";
[Part of this file has been deleted for brevity]
FT /FTId=VAR_002841.
FT VARIANT 132 132 S -> P (in Questembert; highly unstable;
FT causes alpha-thalassemia).
FT /FTId=VAR_002843.
FT VARIANT 134 134 S -> R (in Val de Marne; O(2) affinity
FT up).
FT /FTId=VAR_002844.
FT VARIANT 136 136 V -> E (in Pavie).
FT /FTId=VAR_002845.
FT VARIANT 137 137 L -> M (in Chicago).
FT /FTId=VAR_002846.
FT VARIANT 137 137 L -> P (in Bibba; unstable; causes alpha-
FT thalassemia).
FT /FTId=VAR_002847.
FT VARIANT 137 137 L -> R (in Toyama).
FT /FTId=VAR_035242.
FT VARIANT 139 139 S -> P (in Attleboro; O(2) affinity up).
FT /FTId=VAR_002848.
FT VARIANT 140 140 K -> E (in Hanamaki; O(2) affinity up).
FT /FTId=VAR_002849.
FT VARIANT 140 140 K -> T (in Tokoname; O(2) affinity up).
FT /FTId=VAR_002850.
FT VARIANT 141 141 Y -> H (in Rouen/Ethiopia; O(2) affinity
FT up).
FT /FTId=VAR_002851.
FT VARIANT 142 142 R -> C (in Nunobiki; O(2) affinity up).
FT /FTId=VAR_002852.
FT VARIANT 142 142 R -> H (in Suresnes; O(2) affinity up).
FT /FTId=VAR_002854.
FT VARIANT 142 142 R -> L (in Legnano; O(2) affinity up).
FT /FTId=VAR_002853.
FT VARIANT 142 142 R -> P (in Singapore).
FT /FTId=VAR_002855.
FT CONFLICT 10 10 N -> H (in Ref. 13; BAD97112).
FT HELIX 5 16
FT HELIX 17 21
FT HELIX 22 36
FT HELIX 38 43
FT HELIX 54 72
FT HELIX 74 76
FT HELIX 77 80
FT HELIX 82 90
FT HELIX 97 113
FT TURN 115 117
FT HELIX 120 137
FT TURN 138 140
SQ SEQUENCE 142 AA; 15258 MW; 15E13666573BBBAE CRC64;
MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG
KKVADALTNA VAHVDDMPNA LSALSDLHAH KLRVDPVNFK LLSHCLLVTL AAHLPAEFTP
AVHASLDKFL ASVSTVLTSK YR
//
|
Database entry: tsw:hbb_human
ID HBB_HUMAN Reviewed; 147 AA.
AC P68871; A4GX73; B2ZUE0; P02023; Q13852; Q14481; Q14510; Q45KT0;
AC Q549N7; Q6FI08; Q6R7N2; Q8IZI1; Q9BX96; Q9UCD6; Q9UCP8; Q9UCP9;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 15-JUN-2010, entry version 88.
DE RecName: Full=Hemoglobin subunit beta;
DE AltName: Full=Hemoglobin beta chain;
DE AltName: Full=Beta-globin;
DE Contains:
DE RecName: Full=LVV-hemorphin-7;
GN Name=HBB;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX MEDLINE=77126403; PubMed=1019344;
RA Marotta C., Forget B., Cohen-Solal M., Weissman S.M.;
RT "Nucleotide sequence analysis of coding and noncoding regions of human
RT beta-globin mRNA.";
RL Prog. Nucleic Acid Res. Mol. Biol. 19:165-175(1976).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX MEDLINE=81064667; PubMed=6254664; DOI=10.1016/0092-8674(80)90428-6;
RA Lawn R.M., Efstratiadis A., O'Connell C., Maniatis T.;
RT "The nucleotide sequence of the human beta-globin gene.";
RL Cell 21:647-651(1980).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT LYS-7.
RX PubMed=16175509; DOI=10.1086/491748;
RA Wood E.T., Stover D.A., Slatkin M., Nachman M.W., Hammer M.F.;
RT "The beta-globin recombinational hotspot reduces the effects of strong
RT selection around HbC, a recently arisen mutation providing resistance
RT to malaria.";
RL Am. J. Hum. Genet. 77:637-642(2005).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Lu L., Hu Z.H., Du C.S., Fu Y.S.;
RT "DNA sequence of the human beta-globin gene isolated from a healthy
RT Chinese.";
RL Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT ARG-113.
RA Cabeda J.M., Correia C., Estevinho A., Cardoso C., Amorim M.L.,
RA Cleto E., Vale L., Coimbra E., Pinho L., Justica B.;
RT "Unexpected patterns of globin mutations in thalassemia patients from
RT north of Portugal.";
[Part of this file has been deleted for brevity]
FT VARIANT 141 141 A -> V (in Puttelange; polycythemia; O(2)
FT affinity up).
FT /FTId=VAR_003082.
FT VARIANT 142 142 L -> R (in Olmsted; unstable).
FT /FTId=VAR_003083.
FT VARIANT 143 143 A -> D (in Ohio; O(2) affinity up).
FT /FTId=VAR_003084.
FT VARIANT 144 144 H -> D (in Rancho Mirage).
FT /FTId=VAR_003085.
FT VARIANT 144 144 H -> P (in Syracuse; O(2) affinity up).
FT /FTId=VAR_003087.
FT VARIANT 144 144 H -> Q (in Little Rock; O(2) affinity
FT up).
FT /FTId=VAR_003086.
FT VARIANT 144 144 H -> R (in Abruzzo; O(2) affinity up).
FT /FTId=VAR_003088.
FT VARIANT 145 145 K -> E (in Mito; O(2) affinity up).
FT /FTId=VAR_003089.
FT VARIANT 146 146 Y -> C (in Rainier; O(2) affinity up).
FT /FTId=VAR_003090.
FT VARIANT 146 146 Y -> H (in Bethesda; O(2) affinity up).
FT /FTId=VAR_003091.
FT VARIANT 147 147 H -> D (in Hiroshima; O(2) affinity up).
FT /FTId=VAR_003092.
FT VARIANT 147 147 H -> L (in Cowtown; O(2) affinity up).
FT /FTId=VAR_003093.
FT VARIANT 147 147 H -> P (in York; O(2) affinity up).
FT /FTId=VAR_003094.
FT VARIANT 147 147 H -> Q (in Kodaira; O(2) affinity up).
FT /FTId=VAR_003095.
FT CONFLICT 26 26 Missing (in Ref. 15; ACD39349).
FT CONFLICT 42 42 F -> L (in Ref. 13; AAR96398).
FT HELIX 6 16
FT TURN 21 23
FT HELIX 24 35
FT HELIX 37 42
FT HELIX 44 46
FT HELIX 52 57
FT HELIX 59 77
FT TURN 78 80
FT HELIX 82 94
FT TURN 95 97
FT HELIX 102 119
FT HELIX 120 122
FT HELIX 125 142
FT HELIX 144 146
SQ SEQUENCE 147 AA; 15998 MW; A31F6D621C6556A1 CRC64;
MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
KEFTPPVQAA YQKVVAGVAN ALAHKYH
//
|
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.
Output files for usage example
File: hba_human.matcher
########################################
# Program: matcher
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: matcher
# [-asequence] tsw:hba_human
# [-bsequence] tsw:hbb_human
# Align_format: markx0
# Report_file: hba_human.matcher
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 14
# Extend_penalty: 4
#
# Length: 145
# Identity: 63/145 (43.4%)
# Similarity: 88/145 (60.7%)
# Gaps: 8/145 ( 5.5%)
# Score: 264
#
#
#=======================================
10 20 30 40 50
HBA_HU LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH
:.: .:. : : :::: . : : ::: :. . .: :. .: : :::
HBB_HU LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST
10 20 30 40 50
60 70 80 90
HBA_HU -----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP
:. .:: ::::: : .. .::.:.. . ::.:: :: :::
HBB_HU PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP
60 70 80 90 100
100 110 120 130 140
HBA_HU VNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY
::.:: . :. :: : :::: : :. : .: :. : ::
HBB_HU ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY
110 120 130 140
#---------------------------------------
#---------------------------------------
|
Output files for usage example 2
File: hba_human.matcher
########################################
# Program: matcher
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: matcher
# [-asequence] tsw:hba_human
# [-bsequence] tsw:hbb_human
# -alternatives 10
# Align_format: markx0
# Report_file: hba_human.matcher
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 14
# Extend_penalty: 4
#
# Length: 145
# Identity: 63/145 (43.4%)
# Similarity: 88/145 (60.7%)
# Gaps: 8/145 ( 5.5%)
# Score: 264
#
#
#=======================================
10 20 30 40 50
HBA_HU LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH
:.: .:. : : :::: . : : ::: :. . .: :. .: : :::
HBB_HU LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST
10 20 30 40 50
60 70 80 90
HBA_HU -----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP
:. .:: ::::: : .. .::.:.. . ::.:: :: :::
HBB_HU PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP
60 70 80 90 100
100 110 120 130 140
HBA_HU VNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY
::.:: . :. :: : :::: : :. : .: :. : ::
HBB_HU ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY
110 120 130 140
#=======================================
#
[Part of this file has been deleted for brevity]
#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 14
# Extend_penalty: 4
#
# Length: 12
# Identity: 6/12 (50.0%)
# Similarity: 6/12 (50.0%)
# Gaps: 0/12 ( 0.0%)
# Score: 20
#
#
#=======================================
120
HBA_HU HLPAEFTPAVHA
:: : :: :
HBB_HU HLTPEEKSAVTA
10
#=======================================
#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 14
# Extend_penalty: 4
#
# Length: 21
# Identity: 6/21 (28.6%)
# Similarity: 7/21 (33.3%)
# Gaps: 0/21 ( 0.0%)
# Score: 19
#
#
#=======================================
10 20
HBA_HU PADKTNVKAAWGKVGAHAGEY
: : : : : .:
HBB_HU PVQAAYQKVVAGVANALAHKY
130 140
#---------------------------------------
#---------------------------------------
|
Data files
For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAFULL is used.EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by EMBOSS environment variable EMBOSS_DATA.
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata
Notes
matcher is rigorous but also very slow. The advantage of matcher over water (which is also rigorous) is that it uses far less memory, so you are much less likely to run out of memory when aligning large sequences.
matcher reports a specified number of alignments between the two sequences. water in contrast will only report only the single (optimal) match. The default number of alignments output is 1, but can be increased to (for example) the 10 best alignments by using the -alternatives 10 command-line qualifier. In some cases, for example multidomain proteins or cDNA and genomic DNA comparisons, there may be many interesting and significant alignments.
matcher will not produce an alignment that is guaranteed to be optimal in the same way that water does, which implements the Needleman & Wunsch algorith. water will generate the single, optimal local alignment and uses memory in the order of the product of the lengths of the sequences to be aligned. If you require an optimal alignment you should use water. If you run out of memory or want several possible good alignments, use matcher.
References
- X. Huang and W. Miller (1991) Adv. Appl. Math. 12:373-381
- M. S. Waterman and M. Eggert (J. Mol. Biol. 197:723-728).
Warnings
None.Diagnostic Error Messages
None.Exit status
0 upon successful completion.Known bugs
None.See also
| Program name | Description |
|---|---|
| seqmatchall | All-against-all word comparison of a sequence set |
| 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 |
water will give a single best rigorous local alignment. It will use memory of the order of the product of the lengths of the sequences to be aligned. If you wish the 'best' local alignment you should use water. If you run out of memory or want several possible good alignments, use matcher.
Author(s)
This program was originally written by Bill Pearson as part of the FASTA package under the name 'lalign'.
This application was modified for inclusion in EMBOSS by
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.