| megamerger

## Function

Merge two large overlapping nucleic acid sequences

## Description

megamerger takes two overlapping sequences and merges them into one sequence. It could thus be regarded as the opposite of what splitter does.

The sequences can be very long. The program does a match of all sequence words of size 20 (by default). It then reduces this to the minimum set of overlapping matches by sorting the matches in order of size (largest size first) and then for each such match it removes any smaller matches that overlap. The result is a set of the longest ungapped alignments between the two sequences that do not overlap with each other. If the two sequences are identical in their region of overlap then there will be one region of match and no mismatches.

It should be possible to merge sequences that are Mega bytes long. Compare this with the program merger which does a more accurate alignment of more divergent sequences using the Needle and Wunsch algorithm but which uses much more memory.

The sequences should ideally be identical in their region of overlap. If there are any mismatches between the two sequences then megamerger will still attempt to create a merged sequence, but you should check that this is what you required.

A report of the actions of megamerger is written out. Any actions that require a choice between using regions of the two sequences where they have a mismatch is marked with the word WARNING!. The sequence in these regions is written out in uppercase. All other regions of the output sequence are written in lowercase.

Where there is a mismatch then the sequence that is chosen to supply the region of the mismatch in the final merged sequence is that sequence whose mismatch region is furthest from the start of end of the sequence.

## Usage

Here is a sample session with megamerger

    % megamerger tembl:ap000504 tembl:af129756
    Merge two large overlapping nucleic acid sequences
    Word size [20]:
    Output sequence [ap000504.merged]:
    Output file [ap000504.megamerger]: report

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

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-asequence]         sequence   Sequence USA
      [-bsequence]         sequence   Sequence USA
       -wordsize           integer    Word size
      [-outseq]            seqout     Output sequence USA
      [-outfile]           outfile    Output file name

       Additional (Optional) qualifiers:
       -prefer             boolean    When a mismatch between the two sequence is
                                      discovered, one or other of the two
                                      sequences must be used to create the merged
                                      sequence over this mismatch region. The
                                      default action is to create the merged
                                      sequence using the sequence where the
                                      mismatch is closest to that sequence's
                                      centre. If this option is used, then the
                                      first sequence (seqa) will always be used in
                                      preference to the other sequence when there
                                      is a mismatch.

       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-asequence" associated qualifiers
       -sbegin1             integer    Start of the sequence to be used
       -send1               integer    End of the sequence to be used
       -sreverse1           boolean    Reverse (if DNA)
       -sask1               boolean    Ask for begin/end/reverse
       -snucleotide1        boolean    Sequence is nucleotide
       -sprotein1           boolean    Sequence is protein
       -slower1             boolean    Make lower case
       -supper1             boolean    Make upper case
       -sformat1            string     Input sequence format
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name

       "-bsequence" associated qualifiers
       -sbegin2             integer    Start of the sequence to be used
       -send2               integer    End of the sequence to be used
       -sreverse2           boolean    Reverse (if DNA)
       -sask2               boolean    Ask for begin/end/reverse
       -snucleotide2        boolean    Sequence is nucleotide
       -sprotein2           boolean    Sequence is protein
       -slower2             boolean    Make lower case
       -supper2             boolean    Make upper case
       -sformat2            string     Input sequence format
       -sdbname2            string     Database name
       -sid2                string     Entryname
       -ufo2                string     UFO features
       -fformat2            string     Features format
       -fopenfile2          string     Features file name

       "-outseq" associated 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" associated qualifiers
       -odirectory4         string     Output directory

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for standard and additional values
       -debug               boolean    Write debug output to program.dbg
       -verbose             boolean    Report some/full command line options
       -help                boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning             boolean    Report warnings
       -error               boolean    Report errors
       -fatal               boolean    Report fatal errors
       -die                 boolean    Report deaths

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-asequence] (Parameter 1) | Sequence USA | Readable sequence | Required
[-bsequence] (Parameter 2) | Sequence USA | Readable sequence | Required
-wordsize | Word size | Integer 2 or more | 20
[-outseq] (Parameter 3) | Output sequence USA | Writeable sequence | <sequence>.format
[-outfile] (Parameter 4) | Output file name | Output file | <sequence>.megamerger
Additional (Optional) qualifiers | Allowed values | Default
-prefer | When a mismatch between the two sequence is discovered, one or other of the two sequences must be used to create the merged sequence over this mismatch region. The default action is to create the merged sequence using the sequence where the mismatch is closest to that sequence's centre. If this option is used, then the first sequence (seqa) will always be used in preference to the other sequence when there is a mismatch. | Boolean value Yes/No | No
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

megamerger reads any two Sequence USAs.

### Input files for usage example

'tembl:ap000504' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:ap000504

    ID   AP000504   standard; DNA; HUM; 100000 BP.
    XX
    AC   AP000504; BA000025;
    XX
    SV   AP000504.1
    XX
    DT   28-SEP-1999 (Rel. 61, Created)
    DT   22-AUG-2001 (Rel. 68, Last updated, Version 3)
    XX
    DE   Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section
    DE   3/20.
    XX
    KW   .
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
    XX
    RN   [1]
    RP   1-100000
    RA   Hirakawa M., Yamaguchi H., Imai K., Shimada J.;
    RT   ;
    RL   Submitted (21-SEP-1999) to the EMBL/GenBank/DDBJ databases.
    RL   Mika Hirakawa, Japan Science and Technology Corporation (JST), Advanced
    RL   Databases Department; 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-0081, Japan
    RL   (E-mail:mika@tokyo.jst.go.jp, URL:http://www-alis.tokyo.jst.go.jp/,
    RL   Tel:81-3-5214-8491, Fax:81-3-5214-8470)
    XX
    RN   [2]
    RA   Shiina S., Tamiya G., Oka A., Inoko H.;
    RT   "Homo sapiens 2,229,817bp genomic DNA of 6p21.3 HLA class I region";
    RL   Unpublished.
    XX
    DR   SWISS-PROT; O00299; CLI1_HUMAN.
    DR   SWISS-PROT; O43196; MSH5_HUMAN.
    DR   SWISS-PROT; O95445; APOM_HUMAN.
    DR   SWISS-PROT; O95865; DDH2_HUMAN.
    DR   SWISS-PROT; O95867; NG24_HUMAN.
    DR   SWISS-PROT; P13862; KC2B_HUMAN.
    XX
    CC   This sequence is conducted by Tokai University as a JST sequencing
    CC   Team.
    CC   Principal Investigator: Hidetoshi Inoko Ph.D
    CC   Phone:+81-463-93-1121, Fax:+81-463-94-8884,
    CC   The sequence is submitted by Human Genome Sequencing in ALIS
    CC   project of JST
    CC   Japan Science and Technology Corporation (JST)
    CC   5-3, Yonbancyo, Chiyoda-ku, Tokyo, 102-0081 Japan
    CC   For further infomation about this sequences, please visit our
    CC   sequence archive Web site (http://www-alis.tokyo.jst.go.jp/HGS/top.

      [Part of this file has been deleted for brevity]

         gggtggatca tgaggtcaag agatcgagac tatcctggct aacatgatga aaccccgtct     97080
         ctactaaaaa tacaaaaaat tagctgggca tggtggcggg cacctgtagt cccagctact     97140
         cgggaggctg agtcaggaga atggtgtgaa cccaggagac ggagcttgca gtgagctgag     97200
         gtcgcaccac tgcactccag cctgggtgat agagcgagac tctgtctcaa aaaaaaaaaa     97260
         aaaaaaaaaa aaaacaaaaa ttagccgggt gtggtggcag gcaacttaat cccagctact     97320
         tgggaggcag aggcaggaga atcgtttgaa cctgggaggc ggaggttgaa gagaatagaa     97380
         gctctgctgg tccagagaag gattgggcca gggctctggg agaccaggga gaaagagggc     97440
         acatgtggtc cctgttgact gtgagggtgg gaatctgagg aaggctttgg ctcattgccc     97500
         cttgggtttg tccacagcca tccttcccct gcggagtatg tcgaggtgct ccaggagcta     97560
         cagcggctgg agagtcgcct ccagcccttc ttgcagcgct actacgaggt tctgggtgct     97620
         gctgccacca cggactacaa taacaatgtg agccctttga tggccctgcc ctttctcctc     97680
         agccccagta ctcccaaaac agaacaggct gaaatacaga taactctttc cctccctgga     97740
         aaaacattgc aacagggcca ggtgcagtgg ctcacgcctg taatcccagc actttgggag     97800
         gccaaggtgg gcggatcatc tgagatcggg agtttgagac cagcctggcc aacatggtgc     97860
         aaccccatct ctactgaaaa tataaacatt agctggatgt agtggtgcac acctgtaatc     97920
         ccagctactc aggaggctga ggcaggagaa tcgctagaac tcgggaggag ggggttgcag     97980
         tgagccgaga ttgcactact gcactctagc ctgggtgaca gagcgagact gtctcaaaaa     98040
         acaaaacaaa acaaaaaaac acacattgca acaaaacaat ttctctctaa acctgtaagt     98100
         gattttgtcc tcccttacag agaaggtgat aatctttgct gtaagcactg tcctcgtatc     98160
         gtaccccttg tgcccctgaa tgaatttaga aaatgtaaag tacaggagat cagtatatga     98220
         tgacttactg attcatagta gtgttttaat aggatgttcc ttatgtgaat aagatataat     98280
         ttatttgcaa agatttggtc tacatgtaaa cttccaagga tataactgaa agttttggag     98340
         gacatggtat tctcagtagg cattattgct tttattagtg agatggactc cagcttgata     98400
         ttttctgcct ttttgtgttt ggctggttgt gcgcagcacg agggccggga ggaggatcag     98460
         cggttgatca acttggtagg ggagagcctg cgactgctgg gcaacacctt tgttgcactg     98520
         tctgacctgc gctgcaatct ggcctgcacg cccccacgac acctgcatgt ggtccggcct     98580
         atgtctcact acaccacccc catggtgctc cagcaggcag ccattcccat acaggtgggt     98640
         tagggggagt ctggcctgag ggagagtgag gggtgttgat agagtgaccc agggtagcta     98700
         ctgggcctga aggaggttag gaaaggagga gactggaaac atggtgatga aggctggaga     98760
         tactttagag gtttatcatg aggttttctt ggttaggctc ttgtattttt ctcacatctg     98820
         cctgtccatc tgtctttttc agatcaatgt gggaaccact gtgaccatga caggaaatgg     98880
         gactcggccc cccccaactc ccaatgcaga ggcacctccc cctggtcctg ggcaggcctc     98940
         atccgtggct ccgtcttcta ccaatgtcga gtcctcagct gagggggctc ccccgccagg     99000
         tccagctccc ccgccagcca ccagccaccc gagggtcatc cggatttccc accagagtgt     99060
         ggaacccgtg gtcatgatgc acatgaacat tcaaggtgag aatagttgct ggcgagaaga     99120
         gcaggatcag catgatgagg gaggttcatg ctgaggtgtg agggaacagg gtggggaagg     99180
         gagaggcaca tgctggtggt ggtagcctgg ggaccagagc agaagcttaa gtagacagat     99240
         gtggggggtg tgggggttgg tttgtctttg gaggtgtgtt tgtgtggtga agggagtacc     99300
         tctccctgtt tagatggagg gaaaggcagg ctttctgatt gggggattat gggcctgaag     99360
         tatgcctgat ctcagaagga tatagttagg ccttggccct acctacctca gggccactgt     99420
         ctctgtctcc ctgcccagat tctggcacac agcctggtgg tgttccgagt gctcccactg     99480
         gccccctggg accccctggt catggccaaa ccctgggtaa gagtgagggc atcagggcag     99540
         gctgagctct gggtagagaa agggaagggc tgagtgggtg ggttgaaggg gtccaggttc     99600
         aaggttacat cagacccgcc ccccaggctc caccctcatc cagctgccct ccctgccccc     99660
         tgagttcatg cacgccgtcg cccaccagat cactcatcag gccatggtgg cagctgttgc     99720
         ctccgcggcc gcaggtaatg acctggaagg ggaggcttgg gaggtagggc acagtccatg     99780
         gtggcagctg gctggcaagg gcctggccct cagccctctt cggtctgtct cttctgccac     99840
         ccacaggaca gcaggtgcca ggcttcccaa cagctccaac ccgggtggtg attgcccggc     99900
         ccactcctcc acaggctcgg ccttcccatc ctggagggcc cccagtctct gggacactgg     99960
         tgagcaaggg tcggggagtt ctagtgcgta acagtctagg                          100000
    //

### Database entry: tembl:af129756

    ID   AF129756   standard; DNA; HUM; 184666 BP.
    XX
    AC   AF129756;
    XX
    SV   AF129756.1
    XX
    DT   12-MAR-1999 (Rel. 59, Created)
    DT   29-OCT-1999 (Rel. 61, Last updated, Version 2)
    XX
    DE   Homo sapiens MSH55 gene, partial cds; and CLIC1, DDAH, G6b, G6c, G5b, G6d,
    DE   G6e, G6f, BAT5, G5b, CSK2B, BAT4, G4, Apo M, BAT3, BAT2, AIF-1, 1C7, LST-1,
    DE   LTB, TNF, and LTA genes, complete cds.
    XX
    KW   .
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
    XX
    RN   [1]
    RP   1-184666
    RA   Rowen L., Madan A., Qin S., Shaffer T., James R., Ratcliffe A., Abbasi N.,
    RA   Dickhoff R., Loretz C., Madan A., Dors M., Young J., Lasky S., Hood L.;
    RT   "Sequence of the human major histocompatibility complex class III region";
    RL   Unpublished.
    XX
    RN   [2]
    RP   1-184666
    RA   Rowen L.;
    RT   ;
    RL   Submitted (22-FEB-1999) to the EMBL/GenBank/DDBJ databases.
    RL   Department of Molecular Biotechnology, Box 357730 University of Washington,
    RL   Seattle, WA 98195, USA
    XX
    RN   [3]
    RP   1-184666
    RA   Rowen L.;
    RT   ;
    RL   Submitted (28-OCT-1999) to the EMBL/GenBank/DDBJ databases.
    RL   Multimegabase Sequencing Center, University of Washington, PO Box 357730,
    RL   Seattle, WA 98195, USA
    XX
    DR   EPD; EP11158; HS_TNFA.
    DR   EPD; EP11159; HS_TNFB.
    DR   SPTREMBL; O00452; O00452.
    DR   SPTREMBL; O14931; O14931.
    DR   SPTREMBL; O95866; O95866.
    DR   SPTREMBL; O95868; O95868.
    DR   SPTREMBL; O95869; O95869.
    DR   SPTREMBL; O95870; O95870.

      [Part of this file has been deleted for brevity]

         aaaccagttt accaccactc ctaacactaa acttaaatct gactctaaat gtaagtccaa    181740
         tctgagccac aagcctaaag ttgaacttta tcctgcttta tgaattattc atccattcct    181800
         ccatttagtg agtatctgcg tgcctaacac atgctgggca ttgtcctaag gcaggaggga    181860
         catggaggca aagggatcag agaaggtacc agcacctgtg gagcttgtat tccagtgagg    181920
         ccagacggaa aagaaagaaa ctgaagaaga aattggtact atgagaaaat aagacaggct    181980
         gatgttgtaa gagtggcagg gagctacttt taaatacagt agtcagcaaa atcctctttg    182040
         agtgtttggg tggcactgga gctgagaccc aaatgacaaa aaatagtgac caggtaaaag    182100
         tttgggagca aagcatttca ggtaaaggga gcagctactg caaaggctgg aaggcggaac    182160
         caagctgggg gtgttgacga caaacagaag gccagtgtgg ctggagcaga gagagagact    182220
         gggaggcggg tgggagatga ggtcagagag gagggcaggg gccaggtcat gcagggccat    182280
         gcaagaaggg taaagcctct agatttcatc cagccacagg aagcctttaa aggtcgtcag    182340
         agtgtgtggt gcgtgcgtgt gtgtgtgtgt gtgtgtgtgt gttgcagggg agagaggggg    182400
         agggagagag agagagagag agagaagagg gaggtgagca gaggtgattg gatttttttt    182460
         tcttttgaca tggtgtcttg ctctgtggcc taggctggag tgcagtggca ccatcatagc    182520
         ccactgcaac ctcaaaacca tgggctcaag tcatccttcc acctcagctt cccaagtatc    182580
         taggactaca ggtgtgtgcc actgtgcctg gctaatttta aaaaatattt taaaattttt    182640
         gttgagacag ggtctatgct gctcaggctg gtctcgaact cctggtttca agtgatctgc    182700
         ccatcttggc ctcccaaagt ttttttttgt tagtttgaga ggcggtttcg ctcgttgccc    182760
         aggctggagt gcaatgactg atctcatctc actgcaacct ctgcctcctg ggttcaagcg    182820
         attctcctgc ttcagcctcc caagtagctg ggattacagg tgcatgccac cattcccggc    182880
         taattttttg tatttagtag agatggggtt tcaccatgtt agtcaggctg atctcaaact    182940
         cctgacctca ggtgatccgc ctgcctcagc ctcccaaagt tttgggatta caggtgtgag    183000
         ccaccatgct gggccagcct cccaaagttt tgggattaca ggcatgagtc accacactgg    183060
         ccctggattt tttttctttc ttttttttgg agacggagtc tcactctgtt gcccaggctg    183120
         gagtgcaatg gcgtaatctc agctcactgc aacctctgct gcccgggttc aaacgattct    183180
         cctgtcttag cctcctgagt agctgggatt ataggtgcat gccaccatgc ctggctaatt    183240
         tttgtacttt tagtagagaa agtacaccat cttggccagg ctggtctcga actcctgacc    183300
         tcaggtgatc cacttgcgtc ggcctcccaa agtgctggga ttacaggcgt gagacaccgc    183360
         acccagcctt tttttttttt tttcttttaa gacagaatcg ctctgtcacc caggctggag    183420
         tgcagtggca caatctcggc tcactgcaac ctctgcctcc caggtttaag caatccacct    183480
         atgtcagtct cccaagtagc tgggattata ggtgcatgtc accatgcctg gctaattttt    183540
         gtacttttag tatagaaagt acaccatgtt ggccaggctg gtcttgaact cctgacctca    183600
         agtgatccgc ctgcctcagc ctcccgaagt gctggaatta cagacatgtg ccactgcacc    183660
         cggcctggtt ttttttttct aagagatgga gtctcacttt tctgcccagg ttggagtgca    183720
         atggcaccat catagctcac tgcagccttc aactcttggc ctcaggcaat ccttgcacct    183780
         tagcctcgca gtgttgggat tacaggcatg agccactgag ccttgcctgg actttttttt    183840
         ttttttgaga tggcgtctcg ctctgttgcc caggttggag tgctacggca tgatcttggc    183900
         tcactgcaac ttccacctcc caggttcaag cgattctctt gcctcggccc cccgagtagc    183960
         tgggattaca ggcatgcgcc accgtgcctg gctaattttg gtatttttag tagagatagg    184020
         gtttcatcat gttgggcagg ctggtcttga actcctgacc tcgtgatcca cccacctcgg    184080
         cctcccaaag tgctgggatt ataggcatag ccaacgcgcc cagcctggac ttgtttttaa    184140
         aagatcactg tggctcctgt gtttaggctg gctggtagga gacaggtggc agtggcattg    184200
         atggtgaaga gaaaatagtg gcagccatgg agatggagag aagtagacaa gtttgggata    184260
         tattatacat tccaggggta gaaacaacag gactagatga tggattgatg ggtgggagat    184320
         gtagatactg ggagagaagc aggattctga tggatggaaa aactaaaaaa ttctattttg    184380
         ggtgtggtaa gtctaagtct attagacatg caagtagaga tgtcactggg cagatacaca    184440
         tctggatttc aggggcaagg tccaagctag agaaagaaac ctgggcatgg tcagcatgag    184500
         gatggtgttt aaagccatgg aacttatctt gtgcatccct ataagacccc tttgaggcac    184560
         ttgtttcccc tcacaatgga tgcagtgcat cttccattct gaattccaga ggcaacaacc    184620
         tcctgctcct agaagctaaa ctctccagac ttagtcttct gaattc                   184666
    //

## Output file format

### Output files for usage example

### File: report

    # Report of megamerger of: AP000504 and AF129756

    AP000504 overlap starts at 1
    AF129756 overlap starts at 6036

    Using AF129756 1-6035 as the initial sequence

    Matching region AP000504 1-846 : AF129756 6036-6881
    Length of match: 846

    WARNING!
    Mismatch region found:
    Mismatch AP000504 847-847
    Mismatch AF129756 6882-6882
    Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequence

    Matching region AP000504 848-1794 : AF129756 6883-7829
    Length of match: 947

    WARNING!
    Mismatch region found:
    Mismatch AP000504 1795-1795
    Mismatch AF129756 7830-7830
    Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequence

    Matching region AP000504 1796-2272 : AF129756 7831-8307
    Length of match: 477

    WARNING!
    Mismatch region found:
    Mismatch AP000504 2273-2273
    Mismatch AF129756 8307
    Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequence

    Matching region AP000504 2274-2465 : AF129756 8308-8499
    Length of match: 192

    WARNING!
    Mismatch region found:
    Mismatch AP000504 2466-2466
    Mismatch AF129756 8500-8500
    Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequence

    Matching region AP000504 2467-2654 : AF129756 8501-8688
    Length of match: 188

    WARNING!
    Mismatch region found:
    Mismatch AP000504 2655-2658
    Mismatch AF129756 8688

      [Part of this file has been deleted for brevity]

    WARNING!
    Mismatch region found:
    Mismatch AP000504 95451-95451
    Mismatch AF129756 101481-101481
    Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequence

    Matching region AP000504 95452-96649 : AF129756 101482-102679
    Length of match: 1198

    WARNING!
    Mismatch region found:
    Mismatch AP000504 96650-96650
    Mismatch AF129756 102680-102680
    Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequence

    Matching region AP000504 96651-97272 : AF129756 102681-103302
    Length of match: 622

    WARNING!
    Mismatch region found:
    Mismatch AP000504 97273-97274
    Mismatch AF129756 103302
    Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequence

    Matching region AP000504 97275-97715 : AF129756 103303-103743
    Length of match: 441

    WARNING!
    Mismatch region found:
    Mismatch AP000504 97716-97716
    Mismatch AF129756 103744-103744
    Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequence

    Matching region AP000504 97717-97826 : AF129756 103745-103854
    Length of match: 110

    WARNING!
    Mismatch region found:
    Mismatch AP000504 97827-97827
    Mismatch AF129756 103855-103855
    Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequence

    Matching region AP000504 97828-100000 : AF129756 103856-106028
    Length of match: 2173

    AP000504 overlap ends at 100000
    AF129756 overlap ends at 106028

    Using AF129756 106029-184666 as the final sequence

### File: ap000504.merged

    >AP000504 AP000504.1 Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
    gaattctctccctcccatctgtggctgagattaaagatctgcacctgaagcactgaagaa
    tgtgtgggtaattaaattaccctgccgattcctggagatgctgattacctggagatgacc
    tcagagattatcctaaattaactcctacaagacacacattgcagcgggaggtgaggtagg
    ggaaggattgtgcacctgaggctagcaaaggtttccactctgtttagagatgatgtcacc
    agtgcgtttacatttgcgttgtgttcacacattgagtgctactatgtacaagaccatgtg
    tcagacactgaggtaacaggtatagctactagatagagttcatagctatggaggcaagca
    gattcactgactgctaattctaacatgatgtgacagtgcaactagaaaaacataaacaag
    cactatgtgagcacaaagaaggtgcacatcaactccttacaggtacctgtaaaagccaaa
    gggtaacagttggattgcaccttgaagaggatgcacttttttttttttttaagacagaat
    ctcactctgttgcccaggctggagtgcagtggggcaatctgggctcacttcaacctctac
    ctcccgagttcaagcaattctcctgcctcagcctcctgagtagctggtactagaggcatg
    cgccatgatgctgggctaatttttgtattttcggtagacgtgaagtttcaccaagttggc
    caggctggtcttgaactcctgacctcaaatcatccacccacctcagcctcccaaaatgct
    gagactacaggcgtgagccaccgcgcctgacctggatgtaagattttgataggtacagaa
    caaggaaaagactttccaggccgggcacagtggcttatgcctgtaatcccagcactttgg
    gaggccgaggtgggcagatcacgaggtcagcagttcaagaccagcgtggccaacatggtg
    aaatcccatctctactaaaaatacaaaaattagccaggcatggtggtgggtccctgtaat
    cccagctactccggaggctgaggcaggagaattgcttgaacctgggaggtggaggttgca
    gtgagcaaagaccgcgccactgcactccagcctgggtgacagagggagactccgtctcaa
    aaaaaaaaaaaaaagactttccagaaggagcagcataaacacaggcatgacatgtttcca
    taatggcaagtggccctaaatgactagaatataaggtagatccagtaggaaaggacttag
    aaggggctttggaaggtgagtctggaaattaaaactggggtaaacgtgatggaccctgaa
    catcattatactgcttaagatgctaatcttaatcctgaaggtaatgggaaaacctcctaa
    ggtttatgttattttctttctacttaggctatttaaaaagtggagtgacggccaggcgca
    gtgactcatgcctgtaatcccagcactttgggaggccgaggtgggcggatcaccaggagt
    tcgagaccagcctgaccaacatggtgaaaccccgcctctactgaaaatacaaaaattagc
    caggtgtggtggtgggcgcctgtaatcccagctacttgggaggctgaggcagaagaattg
    cttgaacccgggaagtggaggttgcagtgagcagagatcgtgccattgtactccagcctg
    ggcaacaagagcgaaactcagtcacaaaaaaaaaaaaaaaaaaaaaggagtgacatgctt
    agatctctgttttggaatgacaggttttttgtttctagcatcaatccaaggttcatggct
    tgagaaggtgtactgccagcaatgccattaaccagcaaagggaatgcaggaagaggaaca
    gatctggtgggcatcagtttggatgctctgagtttgagctgcctgtgaaaactgcaggtg
    gtgatatgcaattaacattcacatacggagttcaaaactagagacacaaatttgagagtc
    atcacagaaatgtgaagtgtgttttctataactaaagataaccatgctaacatagccatg
    tgttacattagcattttttttttttttgagacggagtctcactctgttgcccaggctgaa
    gtgcagtgcacaatcttggctcactgcaacctccacctcctgggttcaagcgattctcct
    gccttagtctcctgagtagctggaattacaggcacctaccaacacgcttggctaattttt
    gcattttagtagagatggggctttaccatgttggccagctggtctcaaactcctgacctc
    aagtgattcacccaccttggccccccaaagtgctgggattacaggtgtgagccactgtgc
    ccggccttacattttgtgttttttcctgctgcttgtatgtgtgcaagtctgtgtatcatc
    aatgggtatatgtgtacctgcgctgacaacaaaaaatgagatgcatatcagctactacac
    aaagctgttataaggatgaaatgcagttagccagtgctcagtaaagggcagttgctttac
    tactactaggtggggtggtgtatgtgagaatctgtatactgccattagtaggctttagta
    tgtagtgtgcatatggaattcatgcattagtgtgtagtatgtgtgggacccactcacctg
    agcagcttctctccccacttacagtggcatctgttgaggattcctgtgagggataaggca
    gggagtgaacttgttacaaggcagggacagggaatggaatgtgtttatgtgtctaagctg
    aggcatccaggtcagaggtgctggttgttgaggaagctggcctgggagggcacaaaggca
    gccaaagctggtgcctggccacaaatatgagctgggattaccgtacatggagatggggga
    agggatggacactcacagggacacttagccagaaaaatacacaaagcagacctagttaaa

      [Part of this file has been deleted for brevity]

    accccctaaataaaacttctcctctaccccaacccaaccctgtttctagggctaatcttg
    aaaccagtttaccaccactcctaacactaaacttaaatctgactctaaatgtaagtccaa
    tctgagccacaagcctaaagttgaactttatcctgctttatgaattattcatccattcct
    ccatttagtgagtatctgcgtgcctaacacatgctgggcattgtcctaaggcaggaggga
    catggaggcaaagggatcagagaaggtaccagcacctgtggagcttgtattccagtgagg
    ccagacggaaaagaaagaaactgaagaagaaattggtactatgagaaaataagacaggct
    gatgttgtaagagtggcagggagctacttttaaatacagtagtcagcaaaatcctctttg
    agtgtttgggtggcactggagctgagacccaaatgacaaaaaatagtgaccaggtaaaag
    tttgggagcaaagcatttcaggtaaagggagcagctactgcaaaggctggaaggcggaac
    caagctgggggtgttgacgacaaacagaaggccagtgtggctggagcagagagagagact
    gggaggcgggtgggagatgaggtcagagaggagggcaggggccaggtcatgcagggccat
    gcaagaagggtaaagcctctagatttcatccagccacaggaagcctttaaaggtcgtcag
    agtgtgtggtgcgtgcgtgtgtgtgtgtgtgtgtgtgtgtgttgcaggggagagaggggg
    agggagagagagagagagagagagaagagggaggtgagcagaggtgattggatttttttt
    tcttttgacatggtgtcttgctctgtggcctaggctggagtgcagtggcaccatcatagc
    ccactgcaacctcaaaaccatgggctcaagtcatccttccacctcagcttcccaagtatc
    taggactacaggtgtgtgccactgtgcctggctaattttaaaaaatattttaaaattttt
    gttgagacagggtctatgctgctcaggctggtctcgaactcctggtttcaagtgatctgc
    ccatcttggcctcccaaagtttttttttgttagtttgagaggcggtttcgctcgttgccc
    aggctggagtgcaatgactgatctcatctcactgcaacctctgcctcctgggttcaagcg
    attctcctgcttcagcctcccaagtagctgggattacaggtgcatgccaccattcccggc
    taattttttgtatttagtagagatggggtttcaccatgttagtcaggctgatctcaaact
    cctgacctcaggtgatccgcctgcctcagcctcccaaagttttgggattacaggtgtgag
    ccaccatgctgggccagcctcccaaagttttgggattacaggcatgagtcaccacactgg
    ccctggattttttttctttcttttttttggagacggagtctcactctgttgcccaggctg
    gagtgcaatggcgtaatctcagctcactgcaacctctgctgcccgggttcaaacgattct
    cctgtcttagcctcctgagtagctgggattataggtgcatgccaccatgcctggctaatt
    tttgtacttttagtagagaaagtacaccatcttggccaggctggtctcgaactcctgacc
    tcaggtgatccacttgcgtcggcctcccaaagtgctgggattacaggcgtgagacaccgc
    acccagcctttttttttttttttcttttaagacagaatcgctctgtcacccaggctggag
    tgcagtggcacaatctcggctcactgcaacctctgcctcccaggtttaagcaatccacct
    atgtcagtctcccaagtagctgggattataggtgcatgtcaccatgcctggctaattttt
    gtacttttagtatagaaagtacaccatgttggccaggctggtcttgaactcctgacctca
    agtgatccgcctgcctcagcctcccgaagtgctggaattacagacatgtgccactgcacc
    cggcctggttttttttttctaagagatggagtctcacttttctgcccaggttggagtgca
    atggcaccatcatagctcactgcagccttcaactcttggcctcaggcaatccttgcacct
    tagcctcgcagtgttgggattacaggcatgagccactgagccttgcctggactttttttt
    ttttttgagatggcgtctcgctctgttgcccaggttggagtgctacggcatgatcttggc
    tcactgcaacttccacctcccaggttcaagcgattctcttgcctcggccccccgagtagc
    tgggattacaggcatgcgccaccgtgcctggctaattttggtatttttagtagagatagg
    gtttcatcatgttgggcaggctggtcttgaactcctgacctcgtgatccacccacctcgg
    cctcccaaagtgctgggattataggcatagccaacgcgcccagcctggacttgtttttaa
    aagatcactgtggctcctgtgtttaggctggctggtaggagacaggtggcagtggcattg
    atggtgaagagaaaatagtggcagccatggagatggagagaagtagacaagtttgggata
    tattatacattccaggggtagaaacaacaggactagatgatggattgatgggtgggagat
    gtagatactgggagagaagcaggattctgatggatggaaaaactaaaaaattctattttg
    ggtgtggtaagtctaagtctattagacatgcaagtagagatgtcactgggcagatacaca
    tctggatttcaggggcaaggtccaagctagagaaagaaacctgggcatggtcagcatgag
    gatggtgtttaaagccatggaacttatcttgtgcatccctataagacccctttgaggcac
    ttgtttcccctcacaatggatgcagtgcatcttccattctgaattccagaggcaacaacc
    tcctgctcctagaagctaaactctccagacttagtcttctgaattc

A merged sequence is written out.

Where there has been a mismatch between the two sequences, the merged sequence is written out in uppercase and the sequence whose mismatch region is furthest from the edges of the sequence is used in the merged sequence.

The name and description of the first input sequence is used for the name and description of the output sequence.

A report of the merger is written out.

## Data files

None.

## Notes

If you run out of memory, use a larger wordsize.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

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

Compare this with the program merger which does a more accurate alignment of more divergent sequences using the Needle and Wunsch algorithm but which uses much more memory.

A graphical dotplot of the matches used in this merge can be displayed using the program dotpath.

## Author(s)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

## History

Written Aug 2000 by Gary Williams.

## Target users

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

## Comments

None