|
|
matcher |
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).
Like water, matcher is rigorous, but also very slow. The advantage of matcher is that it uses far less memory than water, so you are much less likely to run out of memory when aligning large sequences.
matcher will also report a specified number of alignments between the two sequences showing the actual local alignments. (water will only report the single best 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 tsw:hba_human tsw:hbb_human Finds the best local alignments between 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 Finds the best local alignments between two sequences Output alignment [hba_human.matcher]: |
Go to the output files for this example
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
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 standard output
-filter boolean Read standard input, write 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
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-asequence] (Parameter 1) |
Sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| [-bsequence] (Parameter 2) |
Sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| [-outfile] (Parameter 3) |
Output alignment file name | Alignment output file | <*>.matcher |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -datafile | 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 | 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 | 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 | 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 | Allowed values | Default | |
| (none) | |||
ID HBA_HUMAN Reviewed; 142 AA.
AC P69905; P01922; Q96KF1; Q9NYR7;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-APR-2007, entry version 41.
DE Hemoglobin subunit alpha (Hemoglobin alpha chain) (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;
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;
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.";
RL Haematologica 86:541-542(2001).
RN [6]
[Part of this file has been deleted for brevity]
FT /FTId=VAR_002840.
FT VARIANT 131 131 A -> D (in Yuda; O(2) affinity down).
FT /FTId=VAR_002842.
FT VARIANT 131 131 A -> P (in Sun Prairie; unstable).
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 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; O(2) affinity 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 HELIX 4 15
FT HELIX 16 20
FT HELIX 21 35
FT HELIX 37 42
FT HELIX 53 71
FT HELIX 73 75
FT HELIX 76 79
FT HELIX 81 89
FT HELIX 96 112
FT TURN 114 116
FT HELIX 119 136
FT TURN 137 139
SQ SEQUENCE 142 AA; 15258 MW; 15E13666573BBBAE CRC64;
MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG
KKVADALTNA VAHVDDMPNA LSALSDLHAH KLRVDPVNFK LLSHCLLVTL AAHLPAEFTP
AVHASLDKFL ASVSTVLTSK YR
//
|
ID HBB_HUMAN Reviewed; 147 AA.
AC P68871; P02023; Q13852; Q14481; Q14510; Q45KT0; Q6FI08; Q8IZI1;
AC Q9BX96; Q9UCP8; Q9UCP9;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 20-MAR-2007, entry version 43.
DE Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin).
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.
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 [2]
RP NUCLEOTIDE SEQUENCE.
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 [3]
RP NUCLEOTIDE SEQUENCE.
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 [4]
RP NUCLEOTIDE SEQUENCE, AND VARIANT DURHAM-N.C. PRO-115.
RC TISSUE=Blood;
RA Kutlar F., Abboud M., Leithner C., Holley L., Brisco J., Kutlar A.;
RT "Electrophoretically silent, very unstable, thalassemic mutation at
RT codon 114 of beta globin (hemoglobin Durham-N.C.) detected by cDNA
RT sequencing of mRNA, from a Russian women.";
RL Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE, AND VARIANT LOUISVILLE LEU-43.
RC TISSUE=Blood;
RA Kutlar F., Harbin J., Brisco J., Kutlar A.;
RT "Rapid detection of electrophoretically silent, unstable human
RT hemoglobin 'Louisville', (Beta; Phe 42 Leu/TTT to CTT) by cDNA
RT sequencing of mRNA.";
RL Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE, AND VARIANT TY GARD GLN-125.
[Part of this file has been deleted for brevity]
FT VARIANT 141 141 A -> T (in St Jacques: O(2) affinity up).
FT /FTId=VAR_003081.
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 HELIX 5 15
FT TURN 20 22
FT HELIX 23 34
FT HELIX 36 41
FT HELIX 43 45
FT HELIX 51 56
FT HELIX 58 76
FT TURN 77 79
FT HELIX 81 93
FT TURN 94 96
FT HELIX 101 118
FT HELIX 119 121
FT HELIX 124 141
FT HELIX 143 145
SQ SEQUENCE 147 AA; 15998 MW; A31F6D621C6556A1 CRC64;
MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
KEFTPPVQAA YQKVVAGVAN ALAHKYH
//
|
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: unknown, multiple, simple, fasta, msf, trace, srs
The available pairwise alignment format names are: pair, markx0, markx1, markx2, markx3, markx10, srspair, score
See: http://emboss.sf.net/docs/themes/AlignFormats.html for further information on alignment formats.
########################################
# Program: matcher
# Rundate: Sun 15 Jul 2007 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
#---------------------------------------
#---------------------------------------
|
########################################
# Program: matcher
# Rundate: Sun 15 Jul 2007 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
#---------------------------------------
#---------------------------------------
|
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:
| Program name | Description |
|---|---|
| seqmatchall | All-against-all comparison of a set of sequences |
| supermatcher | Match large sequences against one or more other sequences |
| water | Smith-Waterman local alignment |
| wordfinder | Match large sequences against one or more other sequences |
| wordmatch | Finds all exact matches of a given size between 2 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.
This application was modified for inclusion in EMBOSS by
Ian Longden (il © sanger.ac.uk)
Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK.