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merger |
Function
Merge two overlapping nucleic acid sequencesDescription
This joins two overlapping nucleic acid sequences into one merged sequence.It uses a global alignment algorithm (Needleman & Wunsch) to optimally align the sequences and then it creates the merged sequence from the alignment. When there is a mismatch in the alignment between the two sequences, the correct base to include in the resulting sequence is chosen by using the base from the sequence which has the best local sequence quality score. The following heuristic is used to find the sequence quality score:
If one of the bases is a 'N', then the other sequence's base is used, else:
A window size around the disputed base is used to find the local quality score. This window size is increased from 5, to 10 to 20 bases or until there is a clear decision on the best choice. If there is no best choice after using a window of 20, then the base in the first sequence is used.
To calculate the quality of a window of a sequence around a base:
- quality = sequence value/length under window either side of the base
- sequence value = sum of points in that window
- unambiguous bases (ACGTU) score 2 points
- ambiguous bases (MRWSYKVHDB) score 1 point
- Ns score 0 points
- off end of the sequence scores 0 points
N.B. This heavily discriminates against the iffy bits at the end of sequence reads.
This program was originally written to aid in the reconstruction of mRNA sequences which had been sequenced from both ends as a 5' and 3' EST (cDNA). eg. joining two reads produced by primer walking sequencing.
Care should be taken to reverse one of the sequences (e.g. using the qualifier '-sreverse2') if this is required to get them both in the correct orientation.
Because it uses a Needleman & Wunsch alignment the required memory may be greater than the available memory when attempting to merge large (cosmid-sized or greater) sequences.
The gap open and gap extension penalties have been set at a higher level than is usual (50 and 5). This was experimentally determined to give the best results with a set of poor quality EST test sequences.
Usage
Here is a sample session with merger
% merger Merge two overlapping nucleic acid sequences Input sequence: tembl:eclacy Second sequence: tembl:eclaca Output alignment [eclacy.merger]: Output sequence [eclacy.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
Standard (Mandatory) qualifiers:
[-asequence] sequence Sequence USA
[-bsequence] sequence Sequence USA
[-outfile] align Output alignment file name
[-outseq] seqout Output sequence USA
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.
-gapopen float Gap opening penalty
-gapextend float Gap extension penalty
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
"-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 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 |
| [-outfile] (Parameter 3) |
Output alignment file name | Alignment output file | |
| [-outseq] (Parameter 4) |
Output sequence USA | Writeable sequence | <sequence>.format |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -datafile | This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA |
| -gapopen | Gap opening penalty | Number from 0.000 to 100.000 | 50.0 |
| -gapextend | Gap extension penalty | Number from 0.000 to 10.000 | 5.0 |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
Input file format
merger reads any two sequence USAs of the same type (protein or nucleic acid.)Input files for usage example
'tembl:eclacy' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:eclacy
ID ECLACY standard; DNA; PRO; 1500 BP.
XX
AC V00295;
XX
SV V00295.1
XX
DT 09-JUN-1982 (Rel. 01, Created)
DT 07-JUL-1995 (Rel. 44, Last updated, Version 4)
XX
DE E. coli lacY gene (codes for lactose permease).
XX
KW membrane protein.
XX
OS Escherichia coli
OC Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
OC Escherichia.
XX
RN [1]
RP 1-1500
RX MEDLINE; 80120651.
RA Buechel D.E., Gronenborn B., Mueller-Hill B.;
RT "Sequence of the lactose permease gene";
RL Nature 283:541-545(1980).
XX
DR SWISS-PROT; P00722; BGAL_ECOLI.
DR SWISS-PROT; P02920; LACY_ECOLI.
DR SWISS-PROT; P07464; THGA_ECOLI.
XX
CC lacZ is a beta-galactosidase and lacA is transacetylase.
CC KST ECO.LACY
XX
FH Key Location/Qualifiers
FH
FT source 1..1500
FT /db_xref="taxon:562"
FT /organism="Escherichia coli"
FT CDS <1..54
FT /codon_start=1
FT /db_xref="SWISS-PROT:P00722"
FT /note="reading frame (lacZ)"
FT /transl_table=11
FT /protein_id="CAA23570.1"
FT /translation="FQLSAGRYHYQLVWCQK"
FT CDS 106..1359
FT /db_xref="SWISS-PROT:P02920"
FT /note="reading frame (lacY)"
FT /transl_table=11
FT /protein_id="CAA23571.1"
FT /translation="MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDT
FT GIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNIL
FT VGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFT
FT INNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKL
FT WFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPL
FT IINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQ
FT FEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFT
FT LSGPGPLSLLRRQVNEVA"
FT CDS 1423..>1500
FT /db_xref="SWISS-PROT:P07464"
FT /note="reading frame (lacA)"
FT /transl_table=11
FT /protein_id="CAA23572.1"
FT /translation="MNMPMTERIRAGKLFTDMCEGLPEKR"
XX
SQ Sequence 1500 BP; 315 A; 342 C; 357 G; 486 T; 0 other;
ttccagctga gcgccggtcg ctaccattac cagttggtct ggtgtcaaaa ataataataa 60
ccgggcaggc catgtctgcc cgtatttcgc gtaaggaaat ccattatgta ctatttaaaa 120
aacacaaact tttggatgtt cggtttattc tttttctttt acttttttat catgggagcc 180
tacttcccgt ttttcccgat ttggctacat gacatcaacc atatcagcaa aagtgatacg 240
ggtattattt ttgccgctat ttctctgttc tcgctattat tccaaccgct gtttggtctg 300
ctttctgaca aactcgggct gcgcaaatac ctgctgtgga ttattaccgg catgttagtg 360
atgtttgcgc cgttctttat ttttatcttc gggccactgt tacaatacaa cattttagta 420
ggatcgattg ttggtggtat ttatctaggc ttttgtttta acgccggtgc gccagcagta 480
gaggcattta ttgagaaagt cagccgtcgc agtaatttcg aatttggtcg cgcgcggatg 540
tttggctgtg ttggctgggc gctgtgtgcc tcgattgtcg gcatcatgtt caccatcaat 600
aatcagtttg ttttctggct gggctctggc tgtgcactca tcctcgccgt tttactcttt 660
ttcgccaaaa cggatgcgcc ctcttctgcc acggttgcca atgcggtagg tgccaaccat 720
tcggcattta gccttaagct ggcactggaa ctgttcagac agccaaaact gtggtttttg 780
tcactgtatg ttattggcgt ttcctgcacc tacgatgttt ttgaccaaca gtttgctaat 840
ttctttactt cgttctttgc taccggtgaa cagggtacgc gggtatttgg ctacgtaacg 900
acaatgggcg aattacttaa cgcctcgatt atgttctttg cgccactgat cattaatcgc 960
atcggtggga aaaacgccct gctgctggct ggcactatta tgtctgtacg tattattggc 1020
tcatcgttcg ccacctcagc gctggaagtg gttattctga aaacgctgca tatgtttgaa 1080
gtaccgttcc tgctggtggg ctgctttaaa tatattacca gccagtttga agtgcgtttt 1140
tcagcgacga tttatctggt ctgtttctgc ttctttaagc aactggcgat gatttttatg 1200
tctgtactgg cgggcaatat gtatgaaagc atcggtttcc agggcgctta tctggtgctg 1260
ggtctggtgg cgctgggctt caccttaatt tccgtgttca cgcttagcgg ccccggcccg 1320
ctttccctgc tgcgtcgtca ggtgaatgaa gtcgcttaag caatcaatgt cggatgcggc 1380
gcgacgctta tccgaccaac atatcataac ggagtgatcg cattgaacat gccaatgacc 1440
gaaagaataa gagcaggcaa gctatttacc gatatgtgcg aaggcttacc ggaaaaaaga 1500
//
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Database entry: tembl:eclaca
ID ECLACA standard; DNA; PRO; 1832 BP.
XX
AC X51872;
XX
SV X51872.1
XX
DT 17-APR-1990 (Rel. 23, Created)
DT 05-JUL-1999 (Rel. 60, Last updated, Version 5)
XX
DE Escherichia coli lacA gene for thiogalactoside transacetylase
XX
KW lac operon; lacA gene; lacY gene; thiogalactoside transacetylase.
XX
OS Escherichia coli
OC Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
OC Escherichia.
XX
RN [1]
RC (1-1832)
RP 1-1832
RX MEDLINE; 86016712.
RA Hediger M.A, Johnson D.F., Nierlich D.P., Zabin I.;
RT "DNA sequence of the lactose operon: The lacA gene and the transcriptional
RT termination region";
RL Proc. Natl. Acad. Sci. U.S.A. 82:6414-6418(1985).
XX
DR REMTREMBL; CAA36161; CAA36161.
DR SWISS-PROT; P07464; THGA_ECOLI.
XX
FH Key Location/Qualifiers
FH
FT source 1..1832
FT /db_xref="taxon:562"
FT /organism="Escherichia coli"
FT CDS <1..18
FT /codon_start=1
FT /db_xref="REMTREMBL:CAA36161"
FT /transl_table=11
FT /product="lacY gene product"
FT /protein_id="CAA36161.1"
FT /translation="VNEVA"
FT CDS 82..693
FT /db_xref="SWISS-PROT:P07464"
FT /transl_table=11
FT /product="thiogalactoside transacetylase"
FT /gene="lacA"
FT /protein_id="CAA36162.1"
FT /translation="MNMPMTERIRAGKLFTDMCEGLPEKRLRGKTLMYEFNHSHPSEVE
FT KRESLIKEMFATVGENAWVEPPVYFSYGSNIHIGRNFYANFNLTIVDDYTVTIGDNVLI
FT APNVTLSVTGHPVHHELRKNGEMYSFPITIGNNVWIGSHVVINPGVTIGDNSVIGAGSI
FT VTKDIPPNVVAAGVPCRVIREINDRDKHYYFKDYKVESSV"
XX
SQ Sequence 1832 BP; 519 A; 510 C; 450 G; 353 T; 0 other;
gtgaatgaag tcgcttaagc aatcaatgtc ggatgcggcg cgacgcttat ccgaccaaca 60
tatcataacg gagtgatcgc attgaacatg ccaatgaccg aaagaataag agcaggcaag 120
ctatttaccg atatgtgcga aggcttaccg gaaaaaagac ttcgtgggaa aacgttaatg 180
tatgagttta atcactcgca tccatcagaa gttgaaaaaa gagaaagcct gattaaagaa 240
atgtttgcca cggtagggga aaacgcctgg gtagaaccgc ctgtctattt ctcttacggt 300
tccaacatcc atataggccg caatttttat gcaaatttca atttaaccat tgtcgatgac 360
tacacggtaa caatcggtga taacgtactg attgcaccca acgttactct ttccgttacg 420
ggacaccctg tacaccatga attgagaaaa aacggcgaga tgtactcttt tccgataacg 480
attggcaata acgtctggat cggaagtcat gtggttatta atccaggcgt caccatcggg 540
gataattctg ttattggcgc gggtagtatc gtcacaaaag acattccacc aaacgtcgtg 600
gcggctggcg ttccttgtcg ggttattcgc gaaataaacg accgggataa gcactattat 660
ttcaaagatt ataaagttga atcgtcagtt taaattataa aaattgcctg atacgctgcg 720
cttatcaggc ctacaagttc agcgatctac attagccgca tccggcatga acaaagcgca 780
ggaacaagcg tcgcatcatg cctctttgac ccacagctgc ggaaaacgta ctggtgcaaa 840
acgcagggtt atgatcatca gcccaacgac gcacagcgca tgaaatgccc agtccatcag 900
gtaattgccg ctgatactac gcagcacgcc agaaaaccac ggggcaagcc cggcgatgat 960
aaaaccgatt ccctgcataa acgccaccag cttgccagca atagccggtt gcacagagtg 1020
atcgagcgcc agcagcaaac agagcggaaa cgcgccgccc agacctaacc cacacaccat 1080
cgcccacaat accggcaatt gcatcggcag ccagataaag ccgcagaacc ccaccagttg 1140
taacaccagc gccagcatta acagtttgcg ccgatcctga tggcgagcca tagcaggcat 1200
cagcaaagct cctgcggctt gcccaagcgt catcaatgcc agtaaggaac cgctgtactg 1260
cgcgctggca ccaatctcaa tatagaaagc gggtaaccag gcaatcaggc tggcgtaacc 1320
gccgttaatc agaccgaagt aaacacccag cgtccacgcg cggggagtga ataccacgcg 1380
aaccggagtg gttgttgtct tgtgggaaga ggcgacctcg cgggcgcttt gccaccacca 1440
ggcaaagagc gcaacaacgg caggcagcgc caccaggcga gtgtttgata ccaggtttcg 1500
ctatgttgaa ctaaccaggg cgttatggcg gcaccaagcc caccgccgcc catcagagcc 1560
gcggaccaca gccccatcac cagtggcgtg cgctgctgaa accgccgttt aatcaccgaa 1620
gcatcaccgc ctgaatgatg ccgatcccca ccccaccaag cagtgcgctg ctaagcagca 1680
gcgcactttg cgggtaaagc tcacgcatca atgcaccgac ggcaatcagc aacagactga 1740
tggcgacact gcgacgttcg ctgacatgct gatgaagcca gcttccggcc agcgccagcc 1800
cgcccatggt aaccaccggc agagcggtcg ac 1832
//
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Output file format
The output sequence file contains the joined sequence, by default in FASTA format. Where there is a mismatch in the alignment, the chosen base is written to the output sequence in uppercase.
The output is a standard EMBOSS alignment file.
The results can be output in one of several styles by using the command-line qualifier -aformat xxx, where 'xxx' is replaced by the name of the required format. Some of the alignment formats can cope with an unlimited number of sequences, while others are only for pairs of sequences.
The available multiple alignment format names are: unknown, multiple, simple, fasta, msf, trace, srs
The available pairwise alignment format names are: pair, markx0, markx1, markx2, markx3, markx10, srspair, score
See: http://emboss.sf.net/docs/themes/AlignFormats.html for further information on alignment formats.
The output report file contains descriptions of the positions where there is a mismatch in the alignment and shows the alignment. Where there is a mismatch in the alignment, the chosen base is written in uppercase.
Output files for usage example
File: eclacy.merger
########################################
# Program: merger
# Rundate: Fri Jul 15 2005 12:00:00
# Align_format: simple
# Report_file: eclacy.merger
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: ECLACY
# 2: ECLACA
# Matrix: EDNAFULL
# Gap_penalty: 50.0
# Extend_penalty: 5.0
#
# Length: 3173
# Identity: 159/3173 ( 5.0%)
# Similarity: 159/3173 ( 5.0%)
# Gaps: 3014/3173 (95.0%)
# Score: 795.0
#
#
#=======================================
ECLACY 1 ttccagctgagcgccggtcgctaccattaccagttggtctggtgtcaaaa 50
ECLACA 1 -------------------------------------------------- 0
ECLACY 51 ataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaat 100
ECLACA 1 -------------------------------------------------- 0
ECLACY 101 ccattatgtactatttaaaaaacacaaacttttggatgttcggtttattc 150
ECLACA 1 -------------------------------------------------- 0
ECLACY 151 tttttcttttacttttttatcatgggagcctacttcccgtttttcccgat 200
ECLACA 1 -------------------------------------------------- 0
ECLACY 201 ttggctacatgacatcaaccatatcagcaaaagtgatacgggtattattt 250
ECLACA 1 -------------------------------------------------- 0
ECLACY 251 ttgccgctatttctctgttctcgctattattccaaccgctgtttggtctg 300
ECLACA 1 -------------------------------------------------- 0
ECLACY 301 ctttctgacaaactcgggctgcgcaaatacctgctgtggattattaccgg 350
[Part of this file has been deleted for brevity]
ECLACA 1310 ctggcgtaaccgccgttaatcagaccgaagtaaacacccagcgtccacgc 1359
ECLACY 1501 -------------------------------------------------- 1500
ECLACA 1360 gcggggagtgaataccacgcgaaccggagtggttgttgtcttgtgggaag 1409
ECLACY 1501 -------------------------------------------------- 1500
ECLACA 1410 aggcgacctcgcgggcgctttgccaccaccaggcaaagagcgcaacaacg 1459
ECLACY 1501 -------------------------------------------------- 1500
ECLACA 1460 gcaggcagcgccaccaggcgagtgtttgataccaggtttcgctatgttga 1509
ECLACY 1501 -------------------------------------------------- 1500
ECLACA 1510 actaaccagggcgttatggcggcaccaagcccaccgccgcccatcagagc 1559
ECLACY 1501 -------------------------------------------------- 1500
ECLACA 1560 cgcggaccacagccccatcaccagtggcgtgcgctgctgaaaccgccgtt 1609
ECLACY 1501 -------------------------------------------------- 1500
ECLACA 1610 taatcaccgaagcatcaccgcctgaatgatgccgatccccaccccaccaa 1659
ECLACY 1501 -------------------------------------------------- 1500
ECLACA 1660 gcagtgcgctgctaagcagcagcgcactttgcgggtaaagctcacgcatc 1709
ECLACY 1501 -------------------------------------------------- 1500
ECLACA 1710 aatgcaccgacggcaatcagcaacagactgatggcgacactgcgacgttc 1759
ECLACY 1501 -------------------------------------------------- 1500
ECLACA 1760 gctgacatgctgatgaagccagcttccggccagcgccagcccgcccatgg 1809
ECLACY 1501 ----------------------- 1500
ECLACA 1810 taaccaccggcagagcggtcgac 1832
#---------------------------------------
#
# Conflicts: ECLACY ECLACA
# position base position base Using
#
#
#---------------------------------------
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File: eclacy.fasta
>ECLACY V00295.1 E. coli lacY gene (codes for lactose permease). ttccagctgagcgccggtcgctaccattaccagttggtctggtgtcaaaaataataataa ccgggcaggccatgtctgcccgtatttcgcgtaaggaaatccattatgtactatttaaaa aacacaaacttttggatgttcggtttattctttttcttttacttttttatcatgggagcc tacttcccgtttttcccgatttggctacatgacatcaaccatatcagcaaaagtgatacg ggtattatttttgccgctatttctctgttctcgctattattccaaccgctgtttggtctg ctttctgacaaactcgggctgcgcaaatacctgctgtggattattaccggcatgttagtg atgtttgcgccgttctttatttttatcttcgggccactgttacaatacaacattttagta ggatcgattgttggtggtatttatctaggcttttgttttaacgccggtgcgccagcagta gaggcatttattgagaaagtcagccgtcgcagtaatttcgaatttggtcgcgcgcggatg tttggctgtgttggctgggcgctgtgtgcctcgattgtcggcatcatgttcaccatcaat aatcagtttgttttctggctgggctctggctgtgcactcatcctcgccgttttactcttt ttcgccaaaacggatgcgccctcttctgccacggttgccaatgcggtaggtgccaaccat tcggcatttagccttaagctggcactggaactgttcagacagccaaaactgtggtttttg tcactgtatgttattggcgtttcctgcacctacgatgtttttgaccaacagtttgctaat ttctttacttcgttctttgctaccggtgaacagggtacgcgggtatttggctacgtaacg acaatgggcgaattacttaacgcctcgattatgttctttgcgccactgatcattaatcgc atcggtgggaaaaacgccctgctgctggctggcactattatgtctgtacgtattattggc tcatcgttcgccacctcagcgctggaagtggttattctgaaaacgctgcatatgtttgaa gtaccgttcctgctggtgggctgctttaaatatattaccagccagtttgaagtgcgtttt tcagcgacgatttatctggtctgtttctgcttctttaagcaactggcgatgatttttatg tctgtactggcgggcaatatgtatgaaagcatcggtttccagggcgcttatctggtgctg ggtctggtggcgctgggcttcaccttaatttccgtgttcacgcttagcggccccggcccg ctttccctgctgcgtcgtcaggtgaatgaagtcgcttaagcaatcaatgtcggatgcggc gcgacgcttatccgaccaacatatcataacggagtgatcgcattgaacatgccaatgacc gaaagaataagagcaggcaagctatttaccgatatgtgcgaaggcttaccggaaaaaaga cttcgtgggaaaacgttaatgtatgagtttaatcactcgcatccatcagaagttgaaaaa agagaaagcctgattaaagaaatgtttgccacggtaggggaaaacgcctgggtagaaccg cctgtctatttctcttacggttccaacatccatataggccgcaatttttatgcaaatttc aatttaaccattgtcgatgactacacggtaacaatcggtgataacgtactgattgcaccc aacgttactctttccgttacgggacaccctgtacaccatgaattgagaaaaaacggcgag atgtactcttttccgataacgattggcaataacgtctggatcggaagtcatgtggttatt aatccaggcgtcaccatcggggataattctgttattggcgcgggtagtatcgtcacaaaa gacattccaccaaacgtcgtggcggctggcgttccttgtcgggttattcgcgaaataaac gaccgggataagcactattatttcaaagattataaagttgaatcgtcagtttaaattata aaaattgcctgatacgctgcgcttatcaggcctacaagttcagcgatctacattagccgc atccggcatgaacaaagcgcaggaacaagcgtcgcatcatgcctctttgacccacagctg cggaaaacgtactggtgcaaaacgcagggttatgatcatcagcccaacgacgcacagcgc atgaaatgcccagtccatcaggtaattgccgctgatactacgcagcacgccagaaaacca cggggcaagcccggcgatgataaaaccgattccctgcataaacgccaccagcttgccagc aatagccggttgcacagagtgatcgagcgccagcagcaaacagagcggaaacgcgccgcc cagacctaacccacacaccatcgcccacaataccggcaattgcatcggcagccagataaa gccgcagaaccccaccagttgtaacaccagcgccagcattaacagtttgcgccgatcctg atggcgagccatagcaggcatcagcaaagctcctgcggcttgcccaagcgtcatcaatgc cagtaaggaaccgctgtactgcgcgctggcaccaatctcaatatagaaagcgggtaacca ggcaatcaggctggcgtaaccgccgttaatcagaccgaagtaaacacccagcgtccacgc gcggggagtgaataccacgcgaaccggagtggttgttgtcttgtgggaagaggcgacctc gcgggcgctttgccaccaccaggcaaagagcgcaacaacggcaggcagcgccaccaggcg agtgtttgataccaggtttcgctatgttgaactaaccagggcgttatggcggcaccaagc ccaccgccgcccatcagagccgcggaccacagccccatcaccagtggcgtgcgctgctga aaccgccgtttaatcaccgaagcatcaccgcctgaatgatgccgatccccaccccaccaa gcagtgcgctgctaagcagcagcgcactttgcgggtaaagctcacgcatcaatgcaccga cggcaatcagcaacagactgatggcgacactgcgacgttcgctgacatgctgatgaagcc agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac |
Data files
It reads the scoring matrix for the alignment from the standard EMBOSS 'data' directory. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences).Notes
None.References
None.Warnings
None.Diagnostic Error Messages
None.Exit status
It exits with a status of 0Known bugs
None.See also
| Program name | Description |
|---|---|
| cons | Creates a consensus from multiple alignments |
| megamerger | Merge two large overlapping nucleic acid sequences |
Author(s)
Gary Williams (gwilliam © rfcgr.mrc.ac.uk)MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK