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|
megamerger
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Merge two large overlapping DNA sequences
Description
megamerger reads two overlapping input DNA sequences and uses a
word-match algorithm to align the sequences. A merged sequence is
generated from the alignment and writen to the output file. The actions
megamerger took in generating the merged sequence are written to an
output file. The sequences can be very long.
Algorithm
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. Where there is a mismatch, the merged sequence uses
bases from the sequence whose mismatch region is furthest from the
start or end of the sequence.
Usage
Here is a sample session with megamerger
% megamerger tembl:v00295 tembl:v00296
Merge two large overlapping DNA sequences
Word size [20]:
output sequence [v00295.merged]:
Output file [v00295.megamerger]: report
Go to the input files for this example
Go to the output files for this example
Command line arguments
Merge two large overlapping DNA sequences
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-asequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
[-bsequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
-wordsize integer [20] Word size (Integer 2 or more)
[-outseq] seqout [.] Sequence filename and
optional format (output USA)
[-outfile] outfile [*.megamerger] Output file name
Additional (Optional) qualifiers:
-prefer boolean [N] 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
-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
"-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 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
Input file format
megamerger reads any two Sequence USAs.
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:v00296
ID V00296; SV 1; linear; genomic DNA; STD; PRO; 3078 BP.
XX
AC V00296;
XX
DT 13-JUL-1983 (Rel. 03, Created)
DT 18-APR-2005 (Rel. 83, Last updated, Version 5)
XX
DE E. coli gene lacZ coding for beta-galactosidase (EC 3.2.1.23).
XX
KW galactosidase.
XX
OS Escherichia coli
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC Enterobacteriaceae; Escherichia.
XX
RN [1]
RP 1-3078
RX PUBMED; 6313347.
RA Kalnins A., Otto K., Ruether U., Mueller-Hill B.;
RT "Sequence of the lacZ gene of Escherichia coli";
RL EMBO J. 2(4):593-597(1983).
XX
RN [2]
RX PUBMED; 3038536.
RA Zell R., Fritz H.J.;
RT "DNA mismatch-repair in Escherichia coli counteracting the hydrolytic
RT deamination of 5-methyl-cytosine residues";
RL EMBO J. 6(6):1809-1815(1987).
XX
CC Data kindly reviewed (18-MAY-1983) by U. Ruether
XX
FH Key Location/Qualifiers
FH
FT source 1..3078
FT /organism="Escherichia coli"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:562"
FT CDS <1..3072
FT /transl_table=11
FT /note="galactosidase"
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"
[Part of this file has been deleted for brevity]
gaggcccgca ccgatcgccc ttcccaacag ttgcgcagcc tgaatggcga atggcgcttt 180
gcctggtttc cggcaccaga agcggtgccg gaaagctggc tggagtgcga tcttcctgag 240
gccgatactg tcgtcgtccc ctcaaactgg cagatgcacg gttacgatgc gcccatctac 300
accaacgtaa cctatcccat tacggtcaat ccgccgtttg ttcccacgga gaatccgacg 360
ggttgttact cgctcacatt taatgttgat gaaagctggc tacaggaagg ccagacgcga 420
attatttttg atggcgttaa ctcggcgttt catctgtggt gcaacgggcg ctgggtcggt 480
tacggccagg acagtcgttt gccgtctgaa tttgacctga gcgcattttt acgcgccgga 540
gaaaaccgcc tcgcggtgat ggtgctgcgt tggagtgacg gcagttatct ggaagatcag 600
gatatgtggc ggatgagcgg cattttccgt gacgtctcgt tgctgcataa accgactaca 660
caaatcagcg atttccatgt tgccactcgc tttaatgatg atttcagccg cgctgtactg 720
gaggctgaag ttcagatgtg cggcgagttg cgtgactacc tacgggtaac agtttcttta 780
tggcagggtg aaacgcaggt cgccagcggc accgcgcctt tcggcggtga aattatcgat 840
gagcgtggtg gttatgccga tcgcgtcaca ctacgtctga acgtcgaaaa cccgaaactg 900
tggagcgccg aaatcccgaa tctctatcgt gcggtggttg aactgcacac cgccgacggc 960
acgctgattg aagcagaagc ctgcgatgtc ggtttccgcg aggtgcggat tgaaaatggt 1020
ctgctgctgc tgaacggcaa gccgttgctg attcgaggcg ttaaccgtca cgagcatcat 1080
cctctgcatg gtcaggtcat ggatgagcag acgatggtgc aggatatcct gctgatgaag 1140
cagaacaact ttaacgccgt gcgctgttcg cattatccga accatccgct gtggtacacg 1200
ctgtgcgacc gctacggcct gtatgtggtg gatgaagcca atattgaaac ccacggcatg 1260
gtgccaatga atcgtctgac cgatgatccg cgctggctac cggcgatgag cgaacgcgta 1320
acgcgaatgg tgcagcgcga tcgtaatcac ccgagtgtga tcatctggtc gctggggaat 1380
gaatcaggcc acggcgctaa tcacgacgcg ctgtatcgct ggatcaaatc tgtcgatcct 1440
tcccgcccgg tgcagtatga aggcggcgga gccgacacca cggccaccga tattatttgc 1500
ccgatgtacg cgcgcgtgga tgaagaccag cccttcccgg ctgtgccgaa atggtccatc 1560
aaaaaatggc tttcgctacc tggagagacg cgcccgctga tcctttgcga atacgcccac 1620
gcgatgggta acagtcttgg cggtttcgct aaatactggc aggcgtttcg tcagtatccc 1680
cgtttacagg gcggcttcgt ctgggactgg gtggatcagt cgctgattaa atatgatgaa 1740
aacggcaacc cgtggtcggc ttacggcggt gattttggcg atacgccgaa cgatcgccag 1800
ttctgtatga acggtctggt ctttgccgac cgcacgccgc atccagcgct gacggaagca 1860
aaacaccagc agcagttttt ccagttccgt ttatccgggc aaaccatcga agtgaccagc 1920
gaatacctgt tccgtcatag cgataacgag ctcctgcact ggatggtggc gctggatggt 1980
aagccgctgg caagcggtga agtgcctctg gatgtcgctc cacaaggtaa acagttgatt 2040
gaactgcctg aactaccgca gccggagagc gccgggcaac tctggctcac agtacgcgta 2100
gtgcaaccga acgcgaccgc atggtcagaa gccgggcaca tcagcgcctg gcagcagtgg 2160
cgtctggcgg aaaacctcag tgtgacgctc cccgccgcgt cccacgccat cccgcatctg 2220
accaccagcg aaatggattt ttgcatcgag ctgggtaata agcgttggca atttaaccgc 2280
cagtcaggct ttctttcaca gatgtggatt ggcgataaaa aacaactgct gacgccgctg 2340
cgcgatcagt tcacccgtgc accgctggat aacgacattg gcgtaagtga agcgacccgc 2400
attgacccta acgcctgggt cgaacgctgg aaggcggcgg gccattacca ggccgaagca 2460
gcgttgttgc agtgcacggc agatacactt gctgatgcgg tgctgattac gaccgctcac 2520
gcgtggcagc atcaggggaa aaccttattt atcagccgga aaacctaccg gattgatggt 2580
agtggtcaaa tggcgattac cgttgatgtt gaagtggcga gcgatacacc gcatccggcg 2640
cggattggcc tgaactgcca gctggcgcag gtagcagagc gggtaaactg gctcggatta 2700
gggccgcaag aaaactatcc cgaccgcctt actgccgcct gttttgaccg ctgggatctg 2760
ccattgtcag acatgtatac cccgtacgtc ttcccgagcg aaaacggtct gcgctgcggg 2820
acgcgcgaat tgaattatgg cccacaccag tggcgcggcg acttccagtt caacatcagc 2880
cgctacagtc aacagcaact gatggaaacc agccatcgcc atctgctgca cgcggaagaa 2940
ggcacatggc tgaatatcga cggtttccat atggggattg gtggcgacga ctcctggagc 3000
ccgtcagtat cggcggaatt ccagctgagc gccggtcgct accattacca gttggtctgg 3060
tgtcaaaaat aataataa 3078
//
Output file format
The actions megamerger took in generating the merged sequence are
written to an output file. Any actions that require a choice between
using regions of the two sequences where they have a mismatch is marked
with the word WARNING!. Where there was a mismatch between the two
sequences, the merged sequence is written out in uppercase and the
sequence whose mismatch region is furthest from the end of the sequence
(the one with most remaining bases or residues) 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.
Output files for usage example
File: report
# Report of megamerger of: V00295 and V00296
V00295 overlap starts at 1
V00296 overlap starts at 3019
Using V00296 1-3018 as the initial sequence
Matching region V00295 1-60 : V00296 3019-3078
Length of match: 60
V00295 overlap ends at 60
V00296 overlap ends at 3078
Using V00295 61-1500 as the final sequence
File: v00295.merged
>V00295 V00295.1 E. coli lacY gene (codes for lactose permease).
accatgattacggattcactggccgtcgttttacaacgtcgtgactgggaaaaccctggc
gttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaa
gaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcttt
gcctggtttccggcaccagaagcggtgccggaaagctggctggagtgcgatcttcctgag
gccgatactgtcgtcgtcccctcaaactggcagatgcacggttacgatgcgcccatctac
accaacgtaacctatcccattacggtcaatccgccgtttgttcccacggagaatccgacg
ggttgttactcgctcacatttaatgttgatgaaagctggctacaggaaggccagacgcga
attatttttgatggcgttaactcggcgtttcatctgtggtgcaacgggcgctgggtcggt
tacggccaggacagtcgtttgccgtctgaatttgacctgagcgcatttttacgcgccgga
gaaaaccgcctcgcggtgatggtgctgcgttggagtgacggcagttatctggaagatcag
gatatgtggcggatgagcggcattttccgtgacgtctcgttgctgcataaaccgactaca
caaatcagcgatttccatgttgccactcgctttaatgatgatttcagccgcgctgtactg
gaggctgaagttcagatgtgcggcgagttgcgtgactacctacgggtaacagtttcttta
tggcagggtgaaacgcaggtcgccagcggcaccgcgcctttcggcggtgaaattatcgat
gagcgtggtggttatgccgatcgcgtcacactacgtctgaacgtcgaaaacccgaaactg
tggagcgccgaaatcccgaatctctatcgtgcggtggttgaactgcacaccgccgacggc
acgctgattgaagcagaagcctgcgatgtcggtttccgcgaggtgcggattgaaaatggt
ctgctgctgctgaacggcaagccgttgctgattcgaggcgttaaccgtcacgagcatcat
cctctgcatggtcaggtcatggatgagcagacgatggtgcaggatatcctgctgatgaag
cagaacaactttaacgccgtgcgctgttcgcattatccgaaccatccgctgtggtacacg
ctgtgcgaccgctacggcctgtatgtggtggatgaagccaatattgaaacccacggcatg
gtgccaatgaatcgtctgaccgatgatccgcgctggctaccggcgatgagcgaacgcgta
acgcgaatggtgcagcgcgatcgtaatcacccgagtgtgatcatctggtcgctggggaat
gaatcaggccacggcgctaatcacgacgcgctgtatcgctggatcaaatctgtcgatcct
tcccgcccggtgcagtatgaaggcggcggagccgacaccacggccaccgatattatttgc
ccgatgtacgcgcgcgtggatgaagaccagcccttcccggctgtgccgaaatggtccatc
aaaaaatggctttcgctacctggagagacgcgcccgctgatcctttgcgaatacgcccac
gcgatgggtaacagtcttggcggtttcgctaaatactggcaggcgtttcgtcagtatccc
cgtttacagggcggcttcgtctgggactgggtggatcagtcgctgattaaatatgatgaa
aacggcaacccgtggtcggcttacggcggtgattttggcgatacgccgaacgatcgccag
ttctgtatgaacggtctggtctttgccgaccgcacgccgcatccagcgctgacggaagca
aaacaccagcagcagtttttccagttccgtttatccgggcaaaccatcgaagtgaccagc
gaatacctgttccgtcatagcgataacgagctcctgcactggatggtggcgctggatggt
aagccgctggcaagcggtgaagtgcctctggatgtcgctccacaaggtaaacagttgatt
gaactgcctgaactaccgcagccggagagcgccgggcaactctggctcacagtacgcgta
gtgcaaccgaacgcgaccgcatggtcagaagccgggcacatcagcgcctggcagcagtgg
cgtctggcggaaaacctcagtgtgacgctccccgccgcgtcccacgccatcccgcatctg
accaccagcgaaatggatttttgcatcgagctgggtaataagcgttggcaatttaaccgc
cagtcaggctttctttcacagatgtggattggcgataaaaaacaactgctgacgccgctg
cgcgatcagttcacccgtgcaccgctggataacgacattggcgtaagtgaagcgacccgc
attgaccctaacgcctgggtcgaacgctggaaggcggcgggccattaccaggccgaagca
gcgttgttgcagtgcacggcagatacacttgctgatgcggtgctgattacgaccgctcac
gcgtggcagcatcaggggaaaaccttatttatcagccggaaaacctaccggattgatggt
agtggtcaaatggcgattaccgttgatgttgaagtggcgagcgatacaccgcatccggcg
cggattggcctgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta
gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccgctgggatctg
ccattgtcagacatgtataccccgtacgtcttcccgagcgaaaacggtctgcgctgcggg
acgcgcgaattgaattatggcccacaccagtggcgcggcgacttccagttcaacatcagc
cgctacagtcaacagcaactgatggaaaccagccatcgccatctgctgcacgcggaagaa
ggcacatggctgaatatcgacggtttccatatggggattggtggcgacgactcctggagc
ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattaccagttggtctgg
tgtcaaaaataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaatcc
attatgtactatttaaaaaacacaaacttttggatgttcggtttattctttttcttttac
ttttttatcatgggagcctacttcccgtttttcccgatttggctacatgacatcaaccat
atcagcaaaagtgatacgggtattatttttgccgctatttctctgttctcgctattattc
caaccgctgtttggtctgctttctgacaaactcgggctgcgcaaatacctgctgtggatt
attaccggcatgttagtgatgtttgcgccgttctttatttttatcttcgggccactgtta
caatacaacattttagtaggatcgattgttggtggtatttatctaggcttttgttttaac
gccggtgcgccagcagtagaggcatttattgagaaagtcagccgtcgcagtaatttcgaa
tttggtcgcgcgcggatgtttggctgtgttggctgggcgctgtgtgcctcgattgtcggc
atcatgttcaccatcaataatcagtttgttttctggctgggctctggctgtgcactcatc
ctcgccgttttactctttttcgccaaaacggatgcgccctcttctgccacggttgccaat
gcggtaggtgccaaccattcggcatttagccttaagctggcactggaactgttcagacag
ccaaaactgtggtttttgtcactgtatgttattggcgtttcctgcacctacgatgttttt
gaccaacagtttgctaatttctttacttcgttctttgctaccggtgaacagggtacgcgg
gtatttggctacgtaacgacaatgggcgaattacttaacgcctcgattatgttctttgcg
ccactgatcattaatcgcatcggtgggaaaaacgccctgctgctggctggcactattatg
tctgtacgtattattggctcatcgttcgccacctcagcgctggaagtggttattctgaaa
acgctgcatatgtttgaagtaccgttcctgctggtgggctgctttaaatatattaccagc
cagtttgaagtgcgtttttcagcgacgatttatctggtctgtttctgcttctttaagcaa
ctggcgatgatttttatgtctgtactggcgggcaatatgtatgaaagcatcggtttccag
ggcgcttatctggtgctgggtctggtggcgctgggcttcaccttaatttccgtgttcacg
cttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaagtcgcttaagca
atcaatgtcggatgcggcgcgacgcttatccgaccaacatatcataacggagtgatcgca
ttgaacatgccaatgaccgaaagaataagagcaggcaagctatttaccgatatgtgcgaa
ggcttaccggaaaaaaga
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
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.
megamerger takes two overlapping sequences and merges them into one
sequence. It could thus be regarded as the opposite of what splitter
does.
References
None.
Warnings
The sequences should ideally be identical in their region of overlap.
If there are any mismatches between the two sequences then megamerger
will still create a merged sequence, but you should check that this is
what you required.
Diagnostic Error Messages
None.
Exit status
It always exits with status 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
merger Merge two overlapping 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 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 (c) emboss.open-bio.org) not to the original author.
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
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