| merger

## 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

Merge two overlapping sequences

## Description

merger reads two overlapping input sequences of the same type (typically nucleotide) and uses a global alignment algorithm (Needleman & Wunsch) to optimally align the sequences. A merged sequence is generated from the alignment and writen to the output file. The sequence alignment is also written.

## Algorithm

It uses a global alignment algorithm (Needleman & Wunsch) to optimally align the sequences and then creates a merged sequence from the alignment. When there is a mismatch in the alignment between the two sequences, the base included in the merged sequence is the base from the sequence which has the best local sequence quality score.

The following heuristic is used to find the sequence quality score. If one of the bases is a 'N', then the other sequence's base is used. Otherwise, a window size around the disputed base is used to find the local quality score. This window size is increased from 5, to 10 to 20 bases or until there is a clear decision on the best choice. If there is no best choice after using a window of 20, then the base in the first sequence is used.

To calculate the quality of a window of a sequence around a base:

        * quality = sequence value/length under window either side of the base
        * sequence value = sum of points in that window
        * unambiguous bases (ACGTU) score 2 points
        * ambiguous bases (MRWSYKVHDB) score 1 point
        * Ns score 0 points
        * off end of the sequence scores 0 points

This heavily discriminates against the iffy bits at the end of sequence reads.

## Usage

Here is a sample session with merger

    % merger
    Merge two overlapping sequences
    Input sequence: tembl:v00295
    Second sequence: tembl:x51872
    Output alignment [v00295.merger]:
    output sequence [v00295.fasta]:

Go to the input files for this example
Go to the output files for this example

Typically, one of the sequences will need to be reverse-complemented to put it into the correct orientation to make it join. For example:

    % merger file1.seq file2.seq -sreverse2 -outseq merged.seq

## Command line arguments

    Merge two overlapping sequences
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers:
      [-asequence]         sequence   Sequence filename and optional format, or
                                      reference (input USA)
      [-bsequence]         sequence   Sequence filename and optional format, or
                                      reference (input USA)
      [-outfile]           align      [*.merger] Output alignment file name
                                      (default -aformat simple)
      [-outseq]            seqout     [.] Sequence filename and
                                      optional format (output USA)

       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.
       -gapopen            float      [@($(acdprotein)? 50.0 : 50.0 )] Gap opening
                                      penalty (Number from 0.000 to 100.000)
       -gapextend          float      [@($(acdprotein)? 5.0 : 5.0)] Gap extension
                                      penalty (Number from 0.000 to 10.000)

       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
       -squick1            boolean    Read id and sequence only
       -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
       -squick2            boolean    Read id and sequence only
       -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

       "-outseq" associated qualifiers
       -osformat4          string     Output seq format
       -osextension4       string     File name extension
       -osname4            string     Base file name
       -osdirectory4       string     Output directory
       -osdbname4          string     Database name to add
       -ossingle4          boolean    Separate file for each entry
       -oufo4              string     UFO features
       -offormat4          string     Features format
       -ofname4            string     Features file name
       -ofdirectory4       string     Output directory

       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 simple) | <*>.merger
[-outseq] (Parameter 4) | seqout | Sequence filename and optional format (output USA) | Writeable sequence | <*>.format
Additional (Optional) qualifiers
-datafile | matrixf | 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 | float | Gap opening penalty | Number from 0.000 to 100.000 | @($(acdprotein)? 50.0 : 50.0 )
-gapextend | float | Gap extension penalty | Number from 0.000 to 10.000 | @($(acdprotein)? 5.0 : 5.0)
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
-squick1 -squick_asequence | boolean | Read id and sequence only | 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
-squick2 -squick_bsequence | boolean | Read id and sequence only | 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 | simple
-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
"-outseq" associated seqout qualifiers
-osformat4 -osformat_outseq | string | Output seq format | Any string |
-osextension4 -osextension_outseq | string | File name extension | Any string |
-osname4 -osname_outseq | string | Base file name | Any string |
-osdirectory4 -osdirectory_outseq | string | Output directory | Any string |
-osdbname4 -osdbname_outseq | string | Database name to add | Any string |
-ossingle4 -ossingle_outseq | boolean | Separate file for each entry | Boolean value Yes/No | N
-oufo4 -oufo_outseq | string | UFO features | Any string |
-offormat4 -offormat_outseq | string | Features format | Any string |
-ofname4 -ofname_outseq | string | Features file name | Any string |
-ofdirectory4 -ofdirectory_outseq | string | Output directory | Any string |
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

merger reads two nucleotide or protein sequences.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier `-sformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

### Input files for usage example

'tembl:v00295' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:v00295

    ID   V00295; SV 1; linear; genomic DNA; STD; PRO; 1500 BP.
    XX
    AC   V00295;
    XX
    DT   09-JUN-1982 (Rel. 01, Created)
    DT   07-JUL-1995 (Rel. 44, Last updated, Version 4)
    XX
    DE   E. coli lacY gene (codes for lactose permease).
    XX
    KW   membrane protein.
    XX
    OS   Escherichia coli
    OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
    OC   Enterobacteriaceae; Escherichia.
    XX
    RN   [1]
    RP   1-1500
    RX   DOI; 10.1038/283541a0.
    RX   PUBMED; 6444453.
    RA   Buechel D.E., Gronenborn B., Mueller-Hill B.;
    RT   "Sequence of the lactose permease gene";
    RL   Nature 283(5747):541-545(1980).
    XX
    CC   lacZ is a beta-galactosidase and lacA is transacetylase.
    CC   KST ECO.LACY
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..1500
    FT                   /organism="Escherichia coli"
    FT                   /mol_type="genomic DNA"
    FT                   /db_xref="taxon:562"
    FT   CDS             <1..54
    FT                   /codon_start=1
    FT                   /transl_table=11
    FT                   /note="reading frame (lacZ)"
    FT                   /db_xref="GOA:P00722"
    FT                   /db_xref="InterPro:IPR004199"
    FT                   /db_xref="InterPro:IPR006101"
    FT                   /db_xref="InterPro:IPR006102"
    FT                   /db_xref="InterPro:IPR006103"
    FT                   /db_xref="InterPro:IPR006104"
    FT                   /db_xref="InterPro:IPR008979"
    FT                   /db_xref="InterPro:IPR011013"
    FT                   /db_xref="InterPro:IPR013781"
    FT                   /db_xref="InterPro:IPR013812"
    FT                   /db_xref="InterPro:IPR014718"
    FT                   /db_xref="InterPro:IPR017853"
    FT                   /db_xref="InterPro:IPR023230"
    FT                   /db_xref="InterPro:IPR023232"

      [Part of this file has been deleted for brevity]

    FT                   /translation="MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDT
    FT                   GIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNIL
    FT                   VGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFT
    FT                   INNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKL
    FT                   WFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPL
    FT                   IINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQ
    FT                   FEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFT
    FT                   LSGPGPLSLLRRQVNEVA"
    FT   CDS             1423..>1500
    FT                   /transl_table=11
    FT                   /note="reading frame (lacA)"
    FT                   /db_xref="GOA:P07464"
    FT                   /db_xref="InterPro:IPR001451"
    FT                   /db_xref="InterPro:IPR011004"
    FT                   /db_xref="InterPro:IPR018357"
    FT                   /db_xref="InterPro:IPR024688"
    FT                   /db_xref="PDB:1KQA"
    FT                   /db_xref="PDB:1KRR"
    FT                   /db_xref="PDB:1KRU"
    FT                   /db_xref="PDB:1KRV"
    FT                   /db_xref="UniProtKB/Swiss-Prot:P07464"
    FT                   /protein_id="CAA23572.1"
    FT                   /translation="MNMPMTERIRAGKLFTDMCEGLPEKR"
    XX
    SQ   Sequence 1500 BP; 315 A; 342 C; 357 G; 486 T; 0 other;
         ttccagctga gcgccggtcg ctaccattac cagttggtct ggtgtcaaaa ataataataa        60
         ccgggcaggc catgtctgcc cgtatttcgc gtaaggaaat ccattatgta ctatttaaaa       120
         aacacaaact tttggatgtt cggtttattc tttttctttt acttttttat catgggagcc       180
         tacttcccgt ttttcccgat ttggctacat gacatcaacc atatcagcaa aagtgatacg       240
         ggtattattt ttgccgctat ttctctgttc tcgctattat tccaaccgct gtttggtctg       300
         ctttctgaca aactcgggct gcgcaaatac ctgctgtgga ttattaccgg catgttagtg       360
         atgtttgcgc cgttctttat ttttatcttc gggccactgt tacaatacaa cattttagta       420
         ggatcgattg ttggtggtat ttatctaggc ttttgtttta acgccggtgc gccagcagta       480
         gaggcattta ttgagaaagt cagccgtcgc agtaatttcg aatttggtcg cgcgcggatg       540
         tttggctgtg ttggctgggc gctgtgtgcc tcgattgtcg gcatcatgtt caccatcaat       600
         aatcagtttg ttttctggct gggctctggc tgtgcactca tcctcgccgt tttactcttt       660
         ttcgccaaaa cggatgcgcc ctcttctgcc acggttgcca atgcggtagg tgccaaccat       720
         tcggcattta gccttaagct ggcactggaa ctgttcagac agccaaaact gtggtttttg       780
         tcactgtatg ttattggcgt ttcctgcacc tacgatgttt ttgaccaaca gtttgctaat       840
         ttctttactt cgttctttgc taccggtgaa cagggtacgc gggtatttgg ctacgtaacg       900
         acaatgggcg aattacttaa cgcctcgatt atgttctttg cgccactgat cattaatcgc       960
         atcggtggga aaaacgccct gctgctggct ggcactatta tgtctgtacg tattattggc      1020
         tcatcgttcg ccacctcagc gctggaagtg gttattctga aaacgctgca tatgtttgaa      1080
         gtaccgttcc tgctggtggg ctgctttaaa tatattacca gccagtttga agtgcgtttt      1140
         tcagcgacga tttatctggt ctgtttctgc ttctttaagc aactggcgat gatttttatg      1200
         tctgtactgg cgggcaatat gtatgaaagc atcggtttcc agggcgctta tctggtgctg      1260
         ggtctggtgg cgctgggctt caccttaatt tccgtgttca cgcttagcgg ccccggcccg      1320
         ctttccctgc tgcgtcgtca ggtgaatgaa gtcgcttaag caatcaatgt cggatgcggc      1380
         gcgacgctta tccgaccaac atatcataac ggagtgatcg cattgaacat gccaatgacc      1440
         gaaagaataa gagcaggcaa gctatttacc gatatgtgcg aaggcttacc ggaaaaaaga      1500
    //

### Database entry: tembl:x51872

    ID   X51872; SV 1; linear; genomic DNA; STD; PRO; 1832 BP.
    XX
    AC   X51872;
    XX
    DT   17-APR-1990 (Rel. 23, Created)
    DT   05-JUL-1999 (Rel. 60, Last updated, Version 5)
    XX
    DE   Escherichia coli lacA gene for thiogalactoside transacetylase
    XX
    KW   lac operon; lacA gene; lacY gene; thiogalactoside transacetylase.
    XX
    OS   Escherichia coli
    OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
    OC   Enterobacteriaceae; Escherichia.
    XX
    RN   [1]
    RC   (1-1832)
    RP   1-1832
    RX   DOI; 10.1073/pnas.82.19.6414.
    RX   PUBMED; 3901000.
    RA   Hediger M.A., Johnson D.F., Nierlich D.P., Zabin I.;
    RT   "DNA sequence of the lactose operon: the lacA gene and the transcriptional
    RT   termination region";
    RL   Proc. Natl. Acad. Sci. U.S.A. 82(19):6414-6418(1985).
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..1832
    FT                   /organism="Escherichia coli"
    FT                   /mol_type="genomic DNA"
    FT                   /db_xref="taxon:562"
    FT   CDS             <1..18
    FT                   /codon_start=1
    FT                   /transl_table=11
    FT                   /product="lacY gene product"
    FT                   /protein_id="CAA36161.1"
    FT                   /translation="VNEVA"
    FT   CDS             82..693
    FT                   /transl_table=11
    FT                   /gene="lacA"
    FT                   /product="thiogalactoside transacetylase"
    FT                   /db_xref="GOA:P07464"
    FT                   /db_xref="InterPro:IPR001451"
    FT                   /db_xref="InterPro:IPR011004"
    FT                   /db_xref="InterPro:IPR018357"
    FT                   /db_xref="InterPro:IPR024688"
    FT                   /db_xref="PDB:1KQA"
    FT                   /db_xref="PDB:1KRR"
    FT                   /db_xref="PDB:1KRU"
    FT                   /db_xref="PDB:1KRV"
    FT                   /db_xref="UniProtKB/Swiss-Prot:P07464"
    FT                   /protein_id="CAA36162.1"
    FT                   /translation="MNMPMTERIRAGKLFTDMCEGLPEKRLRGKTLMYEFNHSHPSEVE
    FT                   KRESLIKEMFATVGENAWVEPPVYFSYGSNIHIGRNFYANFNLTIVDDYTVTIGDNVLI
    FT                   APNVTLSVTGHPVHHELRKNGEMYSFPITIGNNVWIGSHVVINPGVTIGDNSVIGAGSI
    FT                   VTKDIPPNVVAAGVPCRVIREINDRDKHYYFKDYKVESSV"
    XX
    SQ   Sequence 1832 BP; 519 A; 510 C; 450 G; 353 T; 0 other;
         gtgaatgaag tcgcttaagc aatcaatgtc ggatgcggcg cgacgcttat ccgaccaaca        60
         tatcataacg gagtgatcgc attgaacatg ccaatgaccg aaagaataag agcaggcaag       120
         ctatttaccg atatgtgcga aggcttaccg gaaaaaagac ttcgtgggaa aacgttaatg       180
         tatgagttta atcactcgca tccatcagaa gttgaaaaaa gagaaagcct gattaaagaa       240
         atgtttgcca cggtagggga aaacgcctgg gtagaaccgc ctgtctattt ctcttacggt       300
         tccaacatcc atataggccg caatttttat gcaaatttca atttaaccat tgtcgatgac       360
         tacacggtaa caatcggtga taacgtactg attgcaccca acgttactct ttccgttacg       420
         ggacaccctg tacaccatga attgagaaaa aacggcgaga tgtactcttt tccgataacg       480
         attggcaata acgtctggat cggaagtcat gtggttatta atccaggcgt caccatcggg       540
         gataattctg ttattggcgc gggtagtatc gtcacaaaag acattccacc aaacgtcgtg       600
         gcggctggcg ttccttgtcg ggttattcgc gaaataaacg accgggataa gcactattat       660
         ttcaaagatt ataaagttga atcgtcagtt taaattataa aaattgcctg atacgctgcg       720
         cttatcaggc ctacaagttc agcgatctac attagccgca tccggcatga acaaagcgca       780
         ggaacaagcg tcgcatcatg cctctttgac ccacagctgc ggaaaacgta ctggtgcaaa       840
         acgcagggtt atgatcatca gcccaacgac gcacagcgca tgaaatgccc agtccatcag       900
         gtaattgccg ctgatactac gcagcacgcc agaaaaccac ggggcaagcc cggcgatgat       960
         aaaaccgatt ccctgcataa acgccaccag cttgccagca atagccggtt gcacagagtg      1020
         atcgagcgcc agcagcaaac agagcggaaa cgcgccgccc agacctaacc cacacaccat      1080
         cgcccacaat accggcaatt gcatcggcag ccagataaag ccgcagaacc ccaccagttg      1140
         taacaccagc gccagcatta acagtttgcg ccgatcctga tggcgagcca tagcaggcat      1200
         cagcaaagct cctgcggctt gcccaagcgt catcaatgcc agtaaggaac cgctgtactg      1260
         cgcgctggca ccaatctcaa tatagaaagc gggtaaccag gcaatcaggc tggcgtaacc      1320
         gccgttaatc agaccgaagt aaacacccag cgtccacgcg cggggagtga ataccacgcg      1380
         aaccggagtg gttgttgtct tgtgggaaga ggcgacctcg cgggcgcttt gccaccacca      1440
         ggcaaagagc gcaacaacgg caggcagcgc caccaggcga gtgtttgata ccaggtttcg      1500
         ctatgttgaa ctaaccaggg cgttatggcg gcaccaagcc caccgccgcc catcagagcc      1560
         gcggaccaca gccccatcac cagtggcgtg cgctgctgaa accgccgttt aatcaccgaa      1620
         gcatcaccgc ctgaatgatg ccgatcccca ccccaccaag cagtgcgctg ctaagcagca      1680
         gcgcactttg cgggtaaagc tcacgcatca atgcaccgac ggcaatcagc aacagactga      1740
         tggcgacact gcgacgttcg ctgacatgct gatgaagcca gcttccggcc agcgccagcc      1800
         cgcccatggt aaccaccggc agagcggtcg ac                                    1832
    //

## 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 output is a standard EMBOSS sequence file.

The results can be output in one of several styles by using the command-line qualifier `-osformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

### Output files for usage example

### File: v00295.merger

    ########################################
    # Program: merger
    # Rundate: Mon 15 Jul 2013 12:00:00
    # Commandline: merger
    #    -asequence tembl:v00295
    #    -bsequence tembl:x51872
    # Align_format: simple
    # Report_file: v00295.merger
    ########################################

    #=======================================
    #
    # Aligned_sequences: 2
    # 1: V00295
    # 2: X51872
    # Matrix: EDNAFULL
    # Gap_penalty: 50.0
    # Extend_penalty: 5.0
    #
    # Length: 3173
    # Identity:     159/3173 ( 5.0%)
    # Similarity:   159/3173 ( 5.0%)
    # Gaps:        3014/3173 (95.0%)
    # Score: 795.0
    #
    #
    #=======================================

    V00295             1 ttccagctgagcgccggtcgctaccattaccagttggtctggtgtcaaaa     50

    X51872             1 --------------------------------------------------      0

    V00295            51 ataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaat    100

    X51872             1 --------------------------------------------------      0

    V00295           101 ccattatgtactatttaaaaaacacaaacttttggatgttcggtttattc    150

    X51872             1 --------------------------------------------------      0

    V00295           151 tttttcttttacttttttatcatgggagcctacttcccgtttttcccgat    200

    X51872             1 --------------------------------------------------      0

    V00295           201 ttggctacatgacatcaaccatatcagcaaaagtgatacgggtattattt    250

    X51872             1 --------------------------------------------------      0

    V00295           251 ttgccgctatttctctgttctcgctattattccaaccgctgtttggtctg    300

      [Part of this file has been deleted for brevity]

    X51872          1310 ctggcgtaaccgccgttaatcagaccgaagtaaacacccagcgtccacgc   1359

    V00295          1501 --------------------------------------------------   1500

    X51872          1360 gcggggagtgaataccacgcgaaccggagtggttgttgtcttgtgggaag   1409

    V00295          1501 --------------------------------------------------   1500

    X51872          1410 aggcgacctcgcgggcgctttgccaccaccaggcaaagagcgcaacaacg   1459

    V00295          1501 --------------------------------------------------   1500

    X51872          1460 gcaggcagcgccaccaggcgagtgtttgataccaggtttcgctatgttga   1509

    V00295          1501 --------------------------------------------------   1500

    X51872          1510 actaaccagggcgttatggcggcaccaagcccaccgccgcccatcagagc   1559

    V00295          1501 --------------------------------------------------   1500

    X51872          1560 cgcggaccacagccccatcaccagtggcgtgcgctgctgaaaccgccgtt   1609

    V00295          1501 --------------------------------------------------   1500

    X51872          1610 taatcaccgaagcatcaccgcctgaatgatgccgatccccaccccaccaa   1659

    V00295          1501 --------------------------------------------------   1500

    X51872          1660 gcagtgcgctgctaagcagcagcgcactttgcgggtaaagctcacgcatc   1709

    V00295          1501 --------------------------------------------------   1500

    X51872          1710 aatgcaccgacggcaatcagcaacagactgatggcgacactgcgacgttc   1759

    V00295          1501 --------------------------------------------------   1500

    X51872          1760 gctgacatgctgatgaagccagcttccggccagcgccagcccgcccatgg   1809

    V00295          1501 -----------------------   1500

    X51872          1810 taaccaccggcagagcggtcgac   1832

    #---------------------------------------
    #
    # Conflicts:          V00295          X51872
    #              position base   position base Using
    #
    #
    #---------------------------------------

### File: v00295.fasta

    >V00295 V00295.1 E. coli lacY gene (codes for lactose permease).
    ttccagctgagcgccggtcgctaccattaccagttggtctggtgtcaaaaataataataa
    ccgggcaggccatgtctgcccgtatttcgcgtaaggaaatccattatgtactatttaaaa
    aacacaaacttttggatgttcggtttattctttttcttttacttttttatcatgggagcc
    tacttcccgtttttcccgatttggctacatgacatcaaccatatcagcaaaagtgatacg
    ggtattatttttgccgctatttctctgttctcgctattattccaaccgctgtttggtctg
    ctttctgacaaactcgggctgcgcaaatacctgctgtggattattaccggcatgttagtg
    atgtttgcgccgttctttatttttatcttcgggccactgttacaatacaacattttagta
    ggatcgattgttggtggtatttatctaggcttttgttttaacgccggtgcgccagcagta
    gaggcatttattgagaaagtcagccgtcgcagtaatttcgaatttggtcgcgcgcggatg
    tttggctgtgttggctgggcgctgtgtgcctcgattgtcggcatcatgttcaccatcaat
    aatcagtttgttttctggctgggctctggctgtgcactcatcctcgccgttttactcttt
    ttcgccaaaacggatgcgccctcttctgccacggttgccaatgcggtaggtgccaaccat
    tcggcatttagccttaagctggcactggaactgttcagacagccaaaactgtggtttttg
    tcactgtatgttattggcgtttcctgcacctacgatgtttttgaccaacagtttgctaat
    ttctttacttcgttctttgctaccggtgaacagggtacgcgggtatttggctacgtaacg
    acaatgggcgaattacttaacgcctcgattatgttctttgcgccactgatcattaatcgc
    atcggtgggaaaaacgccctgctgctggctggcactattatgtctgtacgtattattggc
    tcatcgttcgccacctcagcgctggaagtggttattctgaaaacgctgcatatgtttgaa
    gtaccgttcctgctggtgggctgctttaaatatattaccagccagtttgaagtgcgtttt
    tcagcgacgatttatctggtctgtttctgcttctttaagcaactggcgatgatttttatg
    tctgtactggcgggcaatatgtatgaaagcatcggtttccagggcgcttatctggtgctg
    ggtctggtggcgctgggcttcaccttaatttccgtgttcacgcttagcggccccggcccg
    ctttccctgctgcgtcgtcaggtgaatgaagtcgcttaagcaatcaatgtcggatgcggc
    gcgacgcttatccgaccaacatatcataacggagtgatcgcattgaacatgccaatgacc
    gaaagaataagagcaggcaagctatttaccgatatgtgcgaaggcttaccggaaaaaaga
    cttcgtgggaaaacgttaatgtatgagtttaatcactcgcatccatcagaagttgaaaaa
    agagaaagcctgattaaagaaatgtttgccacggtaggggaaaacgcctgggtagaaccg
    cctgtctatttctcttacggttccaacatccatataggccgcaatttttatgcaaatttc
    aatttaaccattgtcgatgactacacggtaacaatcggtgataacgtactgattgcaccc
    aacgttactctttccgttacgggacaccctgtacaccatgaattgagaaaaaacggcgag
    atgtactcttttccgataacgattggcaataacgtctggatcggaagtcatgtggttatt
    aatccaggcgtcaccatcggggataattctgttattggcgcgggtagtatcgtcacaaaa
    gacattccaccaaacgtcgtggcggctggcgttccttgtcgggttattcgcgaaataaac
    gaccgggataagcactattatttcaaagattataaagttgaatcgtcagtttaaattata
    aaaattgcctgatacgctgcgcttatcaggcctacaagttcagcgatctacattagccgc
    atccggcatgaacaaagcgcaggaacaagcgtcgcatcatgcctctttgacccacagctg
    cggaaaacgtactggtgcaaaacgcagggttatgatcatcagcccaacgacgcacagcgc
    atgaaatgcccagtccatcaggtaattgccgctgatactacgcagcacgccagaaaacca
    cggggcaagcccggcgatgataaaaccgattccctgcataaacgccaccagcttgccagc
    aatagccggttgcacagagtgatcgagcgccagcagcaaacagagcggaaacgcgccgcc
    cagacctaacccacacaccatcgcccacaataccggcaattgcatcggcagccagataaa
    gccgcagaaccccaccagttgtaacaccagcgccagcattaacagtttgcgccgatcctg
    atggcgagccatagcaggcatcagcaaagctcctgcggcttgcccaagcgtcatcaatgc
    cagtaaggaaccgctgtactgcgcgctggcaccaatctcaatatagaaagcgggtaacca
    ggcaatcaggctggcgtaaccgccgttaatcagaccgaagtaaacacccagcgtccacgc
    gcggggagtgaataccacgcgaaccggagtggttgttgtcttgtgggaagaggcgacctc
    gcgggcgctttgccaccaccaggcaaagagcgcaacaacggcaggcagcgccaccaggcg
    agtgtttgataccaggtttcgctatgttgaactaaccagggcgttatggcggcaccaagc
    ccaccgccgcccatcagagccgcggaccacagccccatcaccagtggcgtgcgctgctga
    aaccgccgtttaatcaccgaagcatcaccgcctgaatgatgccgatccccaccccaccaa
    gcagtgcgctgctaagcagcagcgcactttgcgggtaaagctcacgcatcaatgcaccga
    cggcaatcagcaacagactgatggcgacactgcgacgttcgctgacatgctgatgaagcc
    agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac

## Data files

It reads the scoring matrix for the alignment from the standard EMBOSS 'data' directory. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences).

## Notes

This program was originally written to aid in the reconstruction of mRNA sequences which had been sequenced from both ends as a 5' and 3' EST (cDNA). eg. joining two reads produced by primer walking sequencing.

The gap open and gap extension penalties have been set at a higher level than is usual (50 and 5). This was experimentally determined to give the best results with a set of poor quality EST test sequences.

## References

None.

## Warnings

Care should be taken to reverse one of the sequences (e.g. using the qualifier `-sreverse2`) if this is required to get them both in the correct orientation..

merger uses the memory-hungry Needleman & Wunsch alignment. The required memory may be greater than the available memory when attempting to merge large (cosmid-sized or greater) sequences.

## Diagnostic Error Messages

None.

## Exit status

It exits with a status of 0

## Known bugs

None.

## See also

Program name | Description
--- | ---
cons | Create a consensus sequence from a multiple alignment
consambig | Create an ambiguous consensus sequence from a multiple alignment
megamerger | Merge two large overlapping DNA sequences

## Author(s)

Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## History

Written (Gary Williams) 1999

## Target users

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

## Comments

None