EMBOSS: stretcher

| stretcher

## 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

Needleman-Wunsch rapid global alignment of two sequences

## Description

stretcher calculates an optimal global alignment of two sequences using a modification of the classic dynamic programming algorithm which uses linear space. The output is a standard alignment file. The substitution matrix, gap insertion penalty and gap extension penalties used to calculate the alignment may be specified.

## Algorithm

The standard sequence global alignment program using the Needleman & Wunsch algorithm, as implemented in the program needle, requires O(MN) space. 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. So if a 1 kb and a 10 kb sequence take 10 Mega-words of memory to align, you should expect that in order to align a 10 kb sequence and a 1 Mb sequence you will need approximately 10 Giga-words of memory. When using needle 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).

## Usage

Here is a sample session with stretcher

    % stretcher tsw:hba_human tsw:hbb_human
    Needleman-Wunsch rapid global alignment of 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

    Needleman-Wunsch rapid global alignment of two sequences
    Version: EMBOSS:6.5.6.0

       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      [*.stretcher] 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.
       -gapopen            integer    [12 for protein, 16 for nucleic] Gap penalty
                                      (Positive integer)
       -gapextend          integer    [2 for protein, 4 for nucleic] Gap length
                                      penalty (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
       -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

       "-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
       -scircular2         boolean    Sequence is circular
       -sformat2           string     Input sequence format
       -iquery2            string     Input query fields or ID list
       -ioffset2           integer    Input start position offset
       -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) | <*>.stretcher
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
-gapopen | integer | Gap penalty | Positive integer | 12 for protein, 16 for nucleic
-gapextend | integer | Gap length penalty | Positive integer | 2 for protein, 4 for nucleic
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
-scircular1 -scircular_asequence | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat1 -sformat_asequence | string | Input sequence format | Any string |
-iquery1 -iquery_asequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_asequence | integer | Input start position offset | Any integer value | 0
-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
-scircular2 -scircular_bsequence | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat2 -sformat_bsequence | string | Input sequence format | Any string |
-iquery2 -iquery_bsequence | string | Input query fields or ID list | Any string |
-ioffset2 -ioffset_bsequence | integer | Input start position offset | Any integer value | 0
-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 | Y
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

stretcher reads any 2 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   13-JUN-2012, entry version 108.
    DE   RecName: Full=Hemoglobin subunit alpha;
    DE   AltName: Full=Alpha-globin;
    DE   AltName: Full=Hemoglobin alpha chain;
    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   13-JUN-2012, entry version 108.
    DE   RecName: Full=Hemoglobin subunit beta;
    DE   AltName: Full=Beta-globin;
    DE   AltName: Full=Hemoglobin beta chain;
    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.

The default output format is 'markx0'.

### Output files for usage example

### File: hba_human.stretcher

    ########################################
    # Program: stretcher
    # Rundate: Sun 15 Jul 2012 12:00:00
    # Commandline: stretcher
    #    [-asequence] tsw:hba_human
    #    [-bsequence] tsw:hbb_human
    # 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: 149
    # Identity:      65/149 (43.6%)
    # Similarity:    90/149 (60.4%)
    # Gaps:           9/149 ( 6.0%)
    # Score: 277
    #
    #
    #=======================================

                    10        20        30        40
    HBA_HU MV-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-D
           :: :.: .:. : : ::::  .  : : ::: :. . .: :. .:  : :
    HBB_HU MVHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGD
                   10          20        30        40

           50             60        70        80        90
    HBA_HU LSH-----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLR
           ::      :. .:: :::::  : .. .::.:..    . ::.::  ::
    HBB_HU LSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLH
           50        60        70        80        90

               100       110       120       130       140
    HBA_HU VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
           ::: ::.:: . :.  :: :   :::: : :.  : .: :.  :  ::
    HBB_HU VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
          100       110       120       130       140

    #---------------------------------------
    #---------------------------------------

## 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

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.

## References

1. E. Myers and W. Miller, "Optimal Alignments in Linear Space," CABIOS 4, 1 (1988), 11-17.

## Warnings

Demonstration of similarity is not evidence of homology! This program will produce a global alignment even if there is no biological justification for thinking that there might be a common ancestor.

## Diagnostic Error Messages

None.

## Exit status

It exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
est2genome | Align EST sequences to genomic DNA sequence
needle | Needleman-Wunsch global alignment of two sequences
needleall | Many-to-many pairwise alignments of two sequence sets

## 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 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

Completed 13th May 1999.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None