| needle

## Function

Needleman-Wunsch global alignment of two sequences

## Description

needle reads two input sequences and writes their optimal global sequence alignment to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length. The algorithm uses a dynamic programming method to ensure the alignment is optimum, by exploring all possible alignments and choosing the best. A scoring matrix is read that contains values for every possible residue or nucleotide match. Needle finds the alignment with the maximum possible score where the score of an alignment is equal to the sum of the matches taken from the scoring matrix, minus a penalties arising from opening and extending gaps in the aligned sequences. The substitution matrix and gap opening and extension penalties are user-specified.

### Algorithm

The Needleman-Wunsch algorithm is a member of the class of algorithms that can calculate the best score and alignment of two sequences in the order of `mn` steps, where `n` and `m` are the sequence lengths. These dynamic programming algorithms were first developed for protein sequence comparison by Needleman and Wunsch, though similar methods were independently devised during the late 1960's and early 1970's for use in the fields of speech processing and computer science.

An important problem is the treatment of gaps, i.e., spaces inserted to optimise the alignment score. A penalty is subtracted from the score for each gap opened (the 'gap open' penalty) and a penalty is subtracted from the score for the total number of gap spaces multiplied by a cost (the 'gap extension' penalty). Typically, the cost of extending a gap is set to be 5-10 times lower than the cost for opening a gap.

There are two ways to compute a penalty for a gap of n positions :

    gap opening penalty + (n - 1) * gap extension penalty
    gap penalty + n * gap length penalty

The two methods are basically equivalent. The first way is used by EMBOSS and WU-BLAST. The second way is used by NCBI-BLAST, GCG, Staden and CLUSTAL. Fasta for a long time used the first way, but recently shifted to the second.

In a Needleman-Wunsch global alignment, the entire length of each sequence is aligned. The sequences might be partially overlapping or one sequence might be aligned entirely internally to the other. There is no penalty for the hanging ends of the overlap. In bioinformatics, it is usually reasonable to assume that the sequences are incomplete and there should be no penalty for failing to align the missing bases.

## Usage

Here is a sample session with needle

    % needle tsw:hba_human tsw:hbb_human
    Needleman-Wunsch global alignment of two sequences
    Gap opening penalty [10.0]:
    Gap extension penalty [0.5]:
    Output alignment [hba_human.needle]:

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 filename and optional format, or
                                      reference (input USA)
      [-bsequence]         seqall     Sequence(s) filename and optional format, or
                                      reference (input USA)
       -gapopen            float      [10.0 for any sequence] The gap open penalty
                                      is the score taken away when a gap is
                                      created. The best value depends on the
                                      choice of comparison matrix. The default
                                      value assumes you are using the EBLOSUM62
                                      matrix for protein sequences, and the
                                      EDNAFULL matrix for nucleotide sequences.
                                      (Floating point number from 1.0 to 100.0)
       -gapextend          float      [0.5 for any sequence] The 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 open penalty to zero (or
                                      very low) and using the gap extension
                                      penalty to control gap scoring. (Floating
                                      point number from 0.0 to 10.0)
      [-outfile]           align      [*.needle] Output alignment file name

       Additional (Optional) qualifiers:
       -datafile           matrixf    [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.

       Advanced (Unprompted) qualifiers:
       -[no]brief          boolean    [Y] Brief identity and similarity

       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 each sequence to be used
       -send2              integer    End of each 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. 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(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
-gapopen | The gap open penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence

-gapextend

The 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 open penalty to zero (or very low) and using the gap extension penalty to control gap scoring.

Floating point number from 0.0 to 10.0

0.5 for any sequence

[-outfile] (Parameter 3) | Output alignment file name | Alignment output file | <*>.needle
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
Advanced (Unprompted) qualifiers | Allowed values | Default
-[no]brief | Brief identity and similarity | Boolean value Yes/No | Yes

## Input file format

needle 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               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
    //

### Database entry: tsw:hbb_human

    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
    //

## 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.

### Output files for usage example

### File: hba_human.needle

    ########################################
    # Program: needle
    # Rundate: Tue 15 Jul 2008 12:00:00
    # Commandline: needle
    #    [-asequence] tsw:hba_human
    #    [-bsequence] tsw:hbb_human
    # Align_format: srspair
    # Report_file: hba_human.needle
    ########################################

    #=======================================
    #
    # Aligned_sequences: 2
    # 1: HBA_HUMAN
    # 2: HBB_HUMAN
    # Matrix: EBLOSUM62
    # Gap_penalty: 10.0
    # Extend_penalty: 0.5
    #
    # Length: 149
    # Identity:      65/149 (43.6%)
    # Similarity:    90/149 (60.4%)
    # Gaps:           9/149 ( 6.0%)
    # Score: 292.5
    #
    #
    #=======================================

    HBA_HUMAN          1 MV-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-D     48
                         || |:|.:|:.|.|.||||  :..|.|.|||.|:.:.:|.|:.:|..| |
    HBB_HUMAN          1 MVHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGD     48

    HBA_HUMAN         49 LS-----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLR     93
                         ||     .|:.:||.|||||..|.::.:||:|::....:.||:||..||.
    HBB_HUMAN         49 LSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLH     98

    HBA_HUMAN         94 VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR    142
                         |||.||:||.:.|:..||.|...||||.|.|:..|.:|.|:..|..||.
    HBB_HUMAN         99 VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH    147

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

The Identity: is the percentage of identical matches between the two sequences over the reported aligned region (including any gaps in the length).

The Similarity: is the percentage of matches between the two sequences over the reported aligned region (including any gaps in the length).

## Data files

For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAFULL 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 the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

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

needle is a true implementation of the Needleman-Wunsch algorithm and so produces a full path matrix. It therefore cannot be used with genome sized sequences unless you've a lot of memory and a lot of time.

## References

1. Needleman, S. B. and Wunsch, C. D. (1970) J. Mol. Biol. 48, 443-453.
2. Kruskal, J. B. (1983) An overview of squence comparison In D. Sankoff and J. B. Kruskal, (ed.), Time warps, string edits and macromolecules: the theory and practice of sequence comparison, pp. 1-44 Addison Wesley.

## Warnings

needle is for aligning two sequences over their entire length. This works best with closely related sequences. If you use needle to align very distantly-related sequences, it will produce a result but much of the alignment may have little or no biological significance.

A true Needleman Wunsch implementation like needle needs memory proportional to the product of the sequence lengths. For two sequences of length 10,000,000 and 1,000 it therefore needs memory proportional to 10,000,000,000 characters. Two arrays of this size are produced, one of ints and one of floats so multiply that figure by 8 to get the memory usage in bytes. That doesn't include other overheads. Therefore only use water and needle for accurate alignment of reasonably short sequences.

If you run out of memory, try using stretcher instead.

## Diagnostic Error Messages

    Uncaught exception
     Assertion failed
     raised at ajmem.c:xxx

Probably means you have run out of memory. Try using stretcher if this happens.

## Exit status

0 upon successful completion.

## Known bugs

None.

## See also

Program name | Description
--- | ---
est2genome | Align EST sequences to genomic DNA sequence
stretcher | Needleman-Wunsch rapid global alignment of two sequences

When you want an alignment that covers the whole length of both sequences, use needle.

When you are trying to find the best region of similarity between two sequences, use water.

stretcher is a more suitable program to use to find global alignments of very long sequences.

## Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

## History

Completed 8th July 1999.

Modified 26th July 1999 - scoring tweaked.

Modified 22 Oct 2000 - %ID and %Similarity scores added.

## Target users

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

## Comments

None