| merger

## Function

Merge two overlapping nucleic acid sequences

## Description

This joins two overlapping nucleic acid sequences into one merged sequence.

It uses a global alignment algorithm (Needleman & Wunsch) to optimally align the sequences and then it creates the merged sequence from the alignment. When there is a mismatch in the alignment between the two sequences, the correct base to include in the resulting sequence is chosen by using 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, else:

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

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

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.

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.

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

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.

## Usage

Here is a sample session with merger

    % merger
    Merge two overlapping nucleic acid sequences
    Input sequence: tembl:eclacy
    Second sequence: tembl:eclaca
    Output sequence [eclacy.fasta]:
    Output alignment [eclacy.out2]:

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

       Mandatory qualifiers:
      [-seqa]              sequence   Sequence USA
      [-seqb]              sequence   Sequence USA
      [-outseq]            seqout     Output sequence USA
      [-outfile]           align      Output alignment and explanation

       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.
       -gapopen            float      Gap opening penalty
       -gapextend          float      Gap extension penalty

       Advanced qualifiers: (none)
       Associated qualifiers:
      "-seqa" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-seqb" related qualifiers
       -sbegin2             integer    First base used
       -send2               integer    Last base used, def=seq length
       -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
       -sopenfile2          string     Input filename
       -sdbname2            string     Database name
       -sid2                string     Entryname
       -ufo2                string     UFO features
       -fformat2            string     Features format
       -fopenfile2          string     Features file name
      "-outseq" related qualifiers
       -osformat3           string     Output seq format
       -osextension3        string     File name extension
       -osname3             string     Base file name
       -osdirectory3        string     Output directory
       -osdbname3           string     Database name to add
       -ossingle3           boolean    Separate file for each entry
       -oufo3               string     UFO features
       -offormat3           string     Features format
       -ofname3             string     Features file name
       -ofdirectory3        string     Output directory
      "-outfile" related qualifiers
       -aformat4            string     Alignment format
       -aopenfile4          string     Alignment file name
       -aextension4         string     File name extension
       -adirectory4         string     Output directory
       -aname4              string     Base file name
       -awidth4             integer    Alignment width
       -aaccshow4           boolean    Show accession number in the header
       -adesshow4           boolean    Show description in the header
       -ausashow4           boolean    Show the full USA in the alignment
       -aglobal4            boolean    Show the full sequence in alignment

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -verbose             boolean    Report some/full command line options
       -help                boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning             boolean    Report warnings
       -error               boolean    Report errors
       -fatal               boolean    Report fatal errors
       -die                 boolean    Report deaths

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-seqa] (Parameter 1) | Sequence USA | Readable sequence | Required
[-seqb] (Parameter 2) | Sequence USA | Readable sequence | Required
[-outseq] (Parameter 3) | Output sequence USA | Writeable sequence | <sequence>.format
[-outfile] (Parameter 4) | Output alignment and explanation | Alignment output file |
Optional qualifiers | Allowed values | Default
-datafile | This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA
-gapopen | Gap opening penalty | Number from 1.000 to 100.000 | 50.0
-gapextend | Gap extension penalty | Number from 0.100 to 10.000 | 5
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

merger reads any two sequence USAs of the same type (protein or nucleic acid.)

### Input files for usage example

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

### Database entry: tembl:eclacy

    ID   ECLACY     standard; DNA; PRO; 1500 BP.
    XX
    AC   V00295;
    XX
    SV   V00295.1
    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; gamma subdivision; Enterobacteriaceae;
    OC   Escherichia.
    XX
    RN   [1]
    RP   1-1500
    RX   MEDLINE; 80120651.
    RA   Buechel D.E., Gronenborn B., Mueller-Hill B.;
    RT   "Sequence of the lactose permease gene";
    RL   Nature 283:541-545(1980).
    XX
    DR   SWISS-PROT; P00722; BGAL_ECOLI.
    DR   SWISS-PROT; P02920; LACY_ECOLI.
    DR   SWISS-PROT; P07464; THGA_ECOLI.
    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                   /db_xref="taxon:562"
    FT                   /organism="Escherichia coli"
    FT   CDS             <1..54
    FT                   /codon_start=1
    FT                   /db_xref="SWISS-PROT:P00722"
    FT                   /note="reading frame (lacZ)"
    FT                   /transl_table=11
    FT                   /protein_id="CAA23570.1"
    FT                   /translation="FQLSAGRYHYQLVWCQK"
    FT   CDS             106..1359
    FT                   /db_xref="SWISS-PROT:P02920"
    FT                   /note="reading frame (lacY)"
    FT                   /transl_table=11
    FT                   /protein_id="CAA23571.1"
    FT                   /translation="MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDT
    FT                   GIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNIL
    FT                   VGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFT
    FT                   INNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKL
    FT                   WFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPL
    FT                   IINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQ
    FT                   FEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFT
    FT                   LSGPGPLSLLRRQVNEVA"
    FT   CDS             1423..>1500
    FT                   /db_xref="SWISS-PROT:P07464"
    FT                   /note="reading frame (lacA)"
    FT                   /transl_table=11
    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:eclaca

    ID   ECLACA     standard; DNA; PRO; 1832 BP.
    XX
    AC   X51872;
    XX
    SV   X51872.1
    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; gamma subdivision; Enterobacteriaceae;
    OC   Escherichia.
    XX
    RN   [1]
    RC   (1-1832)
    RP   1-1832
    RX   MEDLINE; 86016712.
    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. 82:6414-6418(1985).
    XX
    DR   REMTREMBL; CAA36161; CAA36161.
    DR   SWISS-PROT; P07464; THGA_ECOLI.
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..1832
    FT                   /db_xref="taxon:562"
    FT                   /organism="Escherichia coli"
    FT   CDS             <1..18
    FT                   /codon_start=1
    FT                   /db_xref="REMTREMBL:CAA36161"
    FT                   /transl_table=11
    FT                   /product="lacY gene product"
    FT                   /protein_id="CAA36161.1"
    FT                   /translation="VNEVA"
    FT   CDS             82..693
    FT                   /db_xref="SWISS-PROT:P07464"
    FT                   /transl_table=11
    FT                   /product="thiogalactoside transacetylase"
    FT                   /gene="lacA"
    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 sequence file contains the joined sequence, by default in FASTA format. Where there is a mismatch in the alignment, the chosen base is written to the output sequence in uppercase.

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://www.uk.embnet.org/Software/EMBOSS/Themes/AlignFormats.html for further information on alignment formats.

The output report file contains descriptions of the positions where there is a mismatch in the alignment and shows the alignment. Where there is a mismatch in the alignment, the chosen base is written in uppercase.

### Output files for usage example

### File: eclacy.fasta

    >ECLACY 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

### File: eclacy.out2

    ########################################
    # Program:  merger
    # Rundate:  Thu May 22 10:36:05 2003
    # Align_format: simple
    # Report_file: eclacy.out2
    ########################################
    #=======================================
    #
    # Aligned_sequences: 2
    # 1: ECLACY
    # 2: ECLACA
    # 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
    #
    #
    #=======================================

    ECLACY             1 ttccagctgagcgccggtcgctaccattaccagttggtctggtgtcaaaa     50

    ECLACA             1                                                         0

    ECLACY            51 ataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaat    100

    ECLACA             1                                                         0

    ECLACY           101 ccattatgtactatttaaaaaacacaaacttttggatgttcggtttattc    150

    ECLACA             1                                                         0

    ECLACY           151 tttttcttttacttttttatcatgggagcctacttcccgtttttcccgat    200

    ECLACA             1                                                         0

    ECLACY           201 ttggctacatgacatcaaccatatcagcaaaagtgatacgggtattattt    250

    ECLACA             1                                                         0

    ECLACY           251 ttgccgctatttctctgttctcgctattattccaaccgctgtttggtctg    300

    ECLACA             1                                                         0

    ECLACY           301 ctttctgacaaactcgggctgcgcaaatacctgctgtggattattaccgg    350

      [Part of this file has been deleted for brevity]

    ECLACY          1501                                                      1500

    ECLACA          1310 ctggcgtaaccgccgttaatcagaccgaagtaaacacccagcgtccacgc   1359

    ECLACY          1501                                                      1500

    ECLACA          1360 gcggggagtgaataccacgcgaaccggagtggttgttgtcttgtgggaag   1409

    ECLACY          1501                                                      1500

    ECLACA          1410 aggcgacctcgcgggcgctttgccaccaccaggcaaagagcgcaacaacg   1459

    ECLACY          1501                                                      1500

    ECLACA          1460 gcaggcagcgccaccaggcgagtgtttgataccaggtttcgctatgttga   1509

    ECLACY          1501                                                      1500

    ECLACA          1510 actaaccagggcgttatggcggcaccaagcccaccgccgcccatcagagc   1559

    ECLACY          1501                                                      1500

    ECLACA          1560 cgcggaccacagccccatcaccagtggcgtgcgctgctgaaaccgccgtt   1609

    ECLACY          1501                                                      1500

    ECLACA          1610 taatcaccgaagcatcaccgcctgaatgatgccgatccccaccccaccaa   1659

    ECLACY          1501                                                      1500

    ECLACA          1660 gcagtgcgctgctaagcagcagcgcactttgcgggtaaagctcacgcatc   1709

    ECLACY          1501                                                      1500

    ECLACA          1710 aatgcaccgacggcaatcagcaacagactgatggcgacactgcgacgttc   1759

    ECLACY          1501                                                      1500

    ECLACA          1760 gctgacatgctgatgaagccagcttccggccagcgccagcccgcccatgg   1809

    ECLACY          1501                           1500

    ECLACA          1810 taaccaccggcagagcggtcgac   1832

    #---------------------------------------
    #
    # ECLACY position base		ECLACA position base	Using
    #
    #
    #---------------------------------------

## 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

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It exits with a status of 0

## Known bugs

None.

## See also

Program name | Description
--- | ---
cons | Creates a consensus from multiple alignments
megamerger | Merge two large overlapping nucleic acid sequences

## Author(s)

Gary Williams (gwilliam © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

## 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