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|
merger
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Merge two overlapping sequences
Description
merger reads two overlapping input sequences of the same type
(typically nucleotide) and uses a global alignment algorithm (Needleman
& Wunsch) to optimally align the sequences. A merged sequence is
generated from the alignment and writen to the output file. The
sequence alignment is also written.
Algorithm
It uses a global alignment algorithm (Needleman & Wunsch) to optimally
align the sequences and then creates a merged sequence from the
alignment. When there is a mismatch in the alignment between the two
sequences, the base included in the merged sequence is the base from
the sequence which has the best local sequence quality score.
The following heuristic is used to find the sequence quality score. If
one of the bases is a 'N', then the other sequence's base is used.
Otherwise, a window size around the disputed base is used to find the
local quality score. This window size is increased from 5, to 10 to 20
bases or until there is a clear decision on the best choice. If there
is no best choice after using a window of 20, then the base in the
first sequence is used.
To calculate the quality of a window of a sequence around a base:
* quality = sequence value/length under window either side of the base
* sequence value = sum of points in that window
* unambiguous bases (ACGTU) score 2 points
* ambiguous bases (MRWSYKVHDB) score 1 point
* Ns score 0 points
* off end of the sequence scores 0 points
This heavily discriminates against the iffy bits at the end of sequence
reads.
Usage
Here is a sample session with merger
% merger
Merge two overlapping sequences
Input sequence: tembl:v00295
Second sequence: tembl:x51872
Output alignment [v00295.merger]:
output sequence [v00295.fasta]:
Go to the input files for this example
Go to the output files for this example
Typically, one of the sequences will need to be reverse-complemented to
put it into the correct orientation to make it join. For example:
% merger file1.seq file2.seq -sreverse2 -outseq merged.seq
Command line arguments
Merge two overlapping sequences
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-asequence] sequence Sequence filename and optional format, or
reference (input USA)
[-bsequence] sequence Sequence filename and optional format, or
reference (input USA)
[-outfile] align [*.merger] Output alignment file name
(default -aformat simple)
[-outseq] seqout [.] Sequence filename and
optional format (output USA)
Additional (Optional) qualifiers:
-datafile matrixf [EBLOSUM62 for protein, EDNAFULL for DNA]
This is the scoring matrix file used when
comparing sequences. By default it is the
file 'EBLOSUM62' (for proteins) or the file
'EDNAFULL' (for nucleic sequences). These
files are found in the 'data' directory of
the EMBOSS installation.
-gapopen float [@($(acdprotein)? 50.0 : 50.0 )] Gap opening
penalty (Number from 0.000 to 100.000)
-gapextend float [@($(acdprotein)? 5.0 : 5.0)] Gap extension
penalty (Number from 0.000 to 10.000)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-asequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-bsequence" associated qualifiers
-sbegin2 integer Start of the sequence to be used
-send2 integer End of the sequence to be used
-sreverse2 boolean Reverse (if DNA)
-sask2 boolean Ask for begin/end/reverse
-snucleotide2 boolean Sequence is nucleotide
-sprotein2 boolean Sequence is protein
-slower2 boolean Make lower case
-supper2 boolean Make upper case
-scircular2 boolean Sequence is circular
-squick2 boolean Read id and sequence only
-sformat2 string Input sequence format
-iquery2 string Input query fields or ID list
-ioffset2 integer Input start position offset
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 string Features file name
"-outfile" associated qualifiers
-aformat3 string Alignment format
-aextension3 string File name extension
-adirectory3 string Output directory
-aname3 string Base file name
-awidth3 integer Alignment width
-aaccshow3 boolean Show accession number in the header
-adesshow3 boolean Show description in the header
-ausashow3 boolean Show the full USA in the alignment
-aglobal3 boolean Show the full sequence in alignment
"-outseq" associated qualifiers
-osformat4 string Output seq format
-osextension4 string File name extension
-osname4 string Base file name
-osdirectory4 string Output directory
-osdbname4 string Database name to add
-ossingle4 boolean Separate file for each entry
-oufo4 string UFO features
-offormat4 string Features format
-ofname4 string Features file name
-ofdirectory4 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
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 (c) 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
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