merger

 

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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