Tehdyt toimenpiteet
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merger |
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Function
Merge two overlapping sequencesDescription
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:6.4.0.0
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 [
|
| 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 |
| -sformat1 -sformat_asequence |
string | Input sequence format | Any string | |
| -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 |
| -sformat2 -sformat_bsequence |
string | Input sequence format | Any string | |
| -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="PDB:1BGL"
FT /db_xref="PDB:1BGM"
[Part of this file has been deleted for brevity]
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 /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="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
//
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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="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: Fri 15 Jul 2011 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 0Known 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.