merger

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

## 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]: ```

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 [.] 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 -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 first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit ```

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-asequence]
(Parameter 1)
sequence Sequence filename and optional format, or reference (input USA) Readable sequence Required
[-bsequence]
(Parameter 2)
sequence Sequence filename and optional format, or reference (input USA) Readable sequence Required
[-outfile]
(Parameter 3)
align Output alignment file name (default -aformat simple) <*>.merger
[-outseq]
(Parameter 4)
seqout Sequence filename and optional format (output USA) Writeable sequence <*>.format
-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)
(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
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
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
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
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
-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 // ```

### 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.

### 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.

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.

None.

## Exit status

It exits with a status of 0

## Known bugs

None.

Program name Description
cons Create a consensus sequence from a multiple alignment
consambig Create an ambiguous consensus sequence from a multiple alignment
megamerger Merge two large overlapping DNA sequences

## Author(s)

Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## History

Written (Gary Williams) 1999

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.