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stretcher |
Function
Finds the best global alignment between two sequencesDescription
stretcher calculates a global alignment of two sequences using a modification of the classic dynamic programming algorithm which uses linear space.A global pairwise alignment is one where it is assumed that the two sequences have diverged from a common ancestor and that the program should try to stretch the two sequences, introducing gaps where necessary, in order to show the alignment over the whole length of the two sequences that best illustrates their similarities.
In contrast, a local alignment program like matcher simply finds local, small parts of the two sequences where there is some similarity and makes no assumption about the whole length of the sequence needing to be similar.
The standard sequence global alignment program using the Needleman & Wunsch algorithm, as implemented in the program needle, requires O(MN) space and O(N) time. This is standard computer-science language for it needing an amount of computer memory that is proportional to the product of the two sequences being aligned and taking an amount of time that is proportional to the shorter of the two sequences. So if a 1 kb and a 10 kb sequence take 10 Mega-words of memory and 10 minutes to align, you should expect that in order to align a 10 kb sequence and a 1 Mb sequence you will need appoximately 10 Giga-words of memory and 100 minutes. Computer memory will rapidly be exhausted as the size of the aligned sequences increases.
This program implements the Myers and Miller algorithm for finding an optimal global alignment in an amount of computer memory that is only proportional to the size of the smaller sequence - O(N).
In computing, a benefit is seldom gained without a cost elsewhere. The cost of gaining a memory-efficient alignment is that it takes about twice the amount of time to do the alignment as the Needleman & Wunsch algorithm. In computer-science language the time is approximately O(2N).
Usage
Here is a sample session with stretcher
% stretcher tsw:hba_human tsw:hbb_human Finds the best global alignment between two sequences Output alignment [hba_human.stretcher]: |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-asequence] sequence Sequence USA
[-bsequence] sequence Sequence USA
[-outfile] align Output alignment file name
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.
-gapopen integer Gap penalty
-gapextend integer Gap length penalty
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 deaths
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-asequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
| [-bsequence] (Parameter 2) |
Sequence USA | Readable sequence | Required |
| [-outfile] (Parameter 3) |
Output alignment file name | Alignment output file | |
| 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 |
| -gapopen | Gap penalty | Positive integer | 12 for protein, 16 for nucleic |
| -gapextend | Gap length penalty | Positive integer | 2 for protein, 4 for nucleic |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
Input file format
stretcher reads any 2 sequence USAs of the same type (DNA or protein).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 STANDARD; PRT; 141 AA.
AC P01922;
DT 21-JUL-1986 (Rel. 01, Created)
DT 21-JUL-1986 (Rel. 01, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE HEMOGLOBIN ALPHA CHAIN.
GN HBA1 AND HBA2.
OS Homo sapiens (Human), Pan troglodytes (Chimpanzee), and
OS Pan paniscus (Pygmy chimpanzee) (Bonobo).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN [1]
RP SEQUENCE FROM N.A. (ALPHA-1).
RX MEDLINE; 81088339.
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 SEQUENCE FROM N.A. (ALPHA-2).
RX MEDLINE; 81175088.
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 [3]
RP SEQUENCE FROM N.A. (ALPHA-2).
RX MEDLINE; 80137531.
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 [4]
RP SEQUENCE FROM N.A. (ALPHA-1 AND ALPHA-2).
RA FLINT J., HIGGS D.R.;
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP SEQUENCE.
RA BRAUNITZER G., GEHRING-MULLER R., HILSCHMANN N., HILSE K., HOBOM G.,
RA RUDLOFF V., WITTMANN-LIEBOLD B.;
RT "The constitution of normal adult human haemoglobin.";
RL Hoppe-Seyler's Z. Physiol. Chem. 325:283-286(1961).
RN [6]
RP SEQUENCE.
RA HILL R.J., KONIGSBERG W.;
RT "The structure of human hemoglobin: IV. The chymotryptic digestion of
RT the alpha chain of human hemoglobin.";
RL J. Biol. Chem. 237:3151-3156(1962).
RN [7]
[Part of this file has been deleted for brevity]
FT /FTId=VAR_002841.
FT VARIANT 130 130 A -> D (IN YUDA; O2 AFFINITY DOWN).
FT /FTId=VAR_002842.
FT VARIANT 131 131 S -> P (IN QUESTEMBERT; HIGHLY UNSTABLE;
FT CAUSES ALPHA-THALASSEMIA).
FT /FTId=VAR_002843.
FT VARIANT 133 133 S -> R (IN VAL DE MARNE; O2 AFFINITY UP).
FT /FTId=VAR_002844.
FT VARIANT 135 135 V -> E (IN PAVIE).
FT /FTId=VAR_002845.
FT VARIANT 136 136 L -> M (IN CHICAGO).
FT /FTId=VAR_002846.
FT VARIANT 136 136 L -> P (IN BIBBA; UNSTABLE;
FT CAUSES ALPHA-THALASSEMIA).
FT /FTId=VAR_002847.
FT VARIANT 138 138 S -> P (IN ATTLEBORO; O2 AFFINITY UP).
FT /FTId=VAR_002848.
FT VARIANT 139 139 K -> E (IN HANAKAMI; O2 AFFINITY UP).
FT /FTId=VAR_002849.
FT VARIANT 139 139 K -> T (IN TOKONAME; O2 AFFINITY UP).
FT /FTId=VAR_002850.
FT VARIANT 140 140 Y -> H (IN ROUEN; O2 AFFINITY UP).
FT /FTId=VAR_002851.
FT VARIANT 141 141 R -> C (IN NUNOBIKI; O2 AFFINITY UP).
FT /FTId=VAR_002852.
FT VARIANT 141 141 R -> L (IN LEGNANO; O2 AFFINITY UP).
FT /FTId=VAR_002853.
FT VARIANT 141 141 R -> H (IN SURESNES; O2 AFFINITY UP).
FT /FTId=VAR_002854.
FT VARIANT 141 141 R -> P (IN SINGAPORE).
FT /FTId=VAR_002855.
FT HELIX 4 35
FT HELIX 37 42
FT TURN 44 45
FT TURN 50 51
FT HELIX 53 71
FT TURN 72 74
FT HELIX 76 79
FT TURN 80 80
FT HELIX 81 89
FT TURN 90 91
FT TURN 95 95
FT HELIX 96 112
FT TURN 114 116
FT HELIX 119 136
FT TURN 137 139
SQ SEQUENCE 141 AA; 15126 MW; 5EC7DB1E CRC32;
VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
VHASLDKFLA SVSTVLTSKY R
//
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Database entry: tsw:hbb_human
ID HBB_HUMAN STANDARD; PRT; 146 AA.
AC P02023;
DT 21-JUL-1986 (Rel. 01, Created)
DT 21-JUL-1986 (Rel. 01, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE HEMOGLOBIN BETA CHAIN.
GN HBB.
OS Homo sapiens (Human), Pan troglodytes (Chimpanzee), and
OS Pan paniscus (Pygmy chimpanzee) (Bonobo).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN [1]
RP SEQUENCE.
RC SPECIES=HUMAN;
RA BRAUNITZER G., GEHRING-MULLER R., HILSCHMANN N., HILSE K., HOBOM G.,
RA RUDLOFF V., WITTMANN-LIEBOLD B.;
RT "The constitution of normal adult human haemoglobin.";
RL Hoppe-Seyler's Z. Physiol. Chem. 325:283-286(1961).
RN [2]
RP SEQUENCE FROM N.A.
RC SPECIES=HUMAN;
RX MEDLINE; 81064667.
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 SEQUENCE OF 121-146 FROM N.A.
RC SPECIES=HUMAN;
RX MEDLINE; 85205333.
RA LANG K.M., SPRITZ R.A.;
RT "Cloning specific complete polyadenylylated 3'-terminal cDNA
RT segments.";
RL Gene 33:191-196(1985).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF DEOXYHEMOGLOBIN.
RC SPECIES=HUMAN;
RX MEDLINE; 76027820.
RA FERMI G.;
RT "Three-dimensional fourier synthesis of human deoxyhaemoglobin at
RT 2.5-A resolution: refinement of the atomic model.";
RL J. Mol. Biol. 97:237-256(1975).
RN [5]
RP SEQUENCE.
RC SPECIES=P.TROGLODYTES;
RX MEDLINE; 66071496.
RA RIFKIN D.B., KONIGSBERG W.;
RT "The characterization of the tryptic peptides from the hemoglobin of
RT the chimpanzee (Pan troglodytes).";
RL Biochim. Biophys. Acta 104:457-461(1965).
RN [6]
[Part of this file has been deleted for brevity]
FT VARIANT 140 140 A -> T (IN ST JACQUES: O2 AFFINITY UP).
FT /FTId=VAR_003081.
FT VARIANT 140 140 A -> V (IN PUTTELANGE; POLYCYTHEMIA;
FT O2 AFFINITY UP).
FT /FTId=VAR_003082.
FT VARIANT 141 141 L -> R (IN OLMSTED; UNSTABLE).
FT /FTId=VAR_003083.
FT VARIANT 142 142 A -> D (IN OHIO; O2 AFFINITY UP).
FT /FTId=VAR_003084.
FT VARIANT 143 143 H -> D (IN RANCHO MIRAGE).
FT /FTId=VAR_003085.
FT VARIANT 143 143 H -> Q (IN LITTLE ROCK; O2 AFFINITY UP).
FT /FTId=VAR_003086.
FT VARIANT 143 143 H -> P (IN SYRACUSE; O2 AFFINITY UP).
FT /FTId=VAR_003087.
FT VARIANT 143 143 H -> R (IN ABRUZZO; O2 AFFINITY UP).
FT /FTId=VAR_003088.
FT VARIANT 144 144 K -> E (IN MITO; O2 AFFINITY UP).
FT /FTId=VAR_003089.
FT VARIANT 145 145 Y -> C (IN RAINIER; O2 AFFINITY UP).
FT /FTId=VAR_003090.
FT VARIANT 145 145 Y -> H (IN BETHESDA; O2 AFFINITY UP).
FT /FTId=VAR_003091.
FT VARIANT 146 146 H -> D (IN HIROSHIMA; O2 AFFINITY UP).
FT /FTId=VAR_003092.
FT VARIANT 146 146 H -> L (IN COWTOWN; O2 AFFINITY UP).
FT /FTId=VAR_003093.
FT VARIANT 146 146 H -> P (IN YORK; O2 AFFINITY UP).
FT /FTId=VAR_003094.
FT VARIANT 146 146 H -> Q (IN KODAIRA; O2 AFFINITY UP).
FT /FTId=VAR_003095.
FT HELIX 5 15
FT TURN 16 17
FT HELIX 20 34
FT HELIX 36 41
FT HELIX 43 45
FT HELIX 51 55
FT TURN 56 56
FT HELIX 58 75
FT TURN 76 77
FT HELIX 78 94
FT TURN 95 96
FT TURN 100 100
FT HELIX 101 121
FT HELIX 124 142
FT TURN 143 144
SQ SEQUENCE 146 AA; 15867 MW; EC9744C9 CRC32;
VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
EFTPPVQAAY QKVVAGVANA LAHKYH
//
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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: 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.
The default output format is 'markx0'.
Output files for usage example
File: hba_human.stretcher
########################################
# Program: stretcher
# Rundate: Fri Jul 15 2005 12:00:00
# Align_format: markx0
# Report_file: hba_human.stretcher
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 12
# Extend_penalty: 2
#
# Length: 148
# Identity: 64/148 (43.2%)
# Similarity: 89/148 (60.1%)
# Gaps: 9/148 ( 6.1%)
# Score: 272
#
#
#=======================================
10 20 30 40
HBA_HU V-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DL
: :.: .:. : : :::: . : : ::: :. . .: :. .: : ::
HBB_HU VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDL
10 20 30 40
50 60 70 80 90
HBA_HU SH-----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRV
: :. .:: ::::: : .. .::.:.. . ::.:: :: :
HBB_HU STPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHV
50 60 70 80 90
100 110 120 130 140
HBA_HU DPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
:: ::.:: . :. :: : :::: : :. : .: :. : ::
HBB_HU DPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
100 110 120 130 140
#---------------------------------------
#---------------------------------------
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Data files
For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAMAT is used. Others can be specified.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
None.References
Warnings
This program will produce a global alignment even if there is no biological justification for thinking that there might be a common ancestor.Demonstration of similarity is not evidence of homology!
Diagnostic Error Messages
None.Exit status
It exits with a status of 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| est2genome | Align EST and genomic DNA sequences |
| needle | Needleman-Wunsch global alignment |
Author(s)
The original program was written by Gene Myers and Webb Miller in 1989.
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.