merger.txt

emboss的linux版本的源代码

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="MNMPMTERIRAGKLFTDMCEGLPEKRLRGKTLMYEFNHSHPSEV
E
FT                   KRESLIKEMFATVGENAWVEPPVYFSYGSNIHIGRNFYANFNLTIVDDYTVTIGDNVL
I
FT                   APNVTLSVTGHPVHHELRKNGEMYSFPITIGNNVWIGSHVVINPGVTIGDNSVIGAGS
I
FT                   VTKDIPPNVVAAGVPCRVIREINDRDKHYYFKDYKVESSV"
XX
SQ   Sequence 1832 BP; 519 A; 510 C; 450 G; 353 T; 0 other;
     gtgaatgaag tcgcttaagc aatcaatgtc ggatgcggcg cgacgcttat ccgaccaaca        6
0
     tatcataacg gagtgatcgc attgaacatg ccaatgaccg aaagaataag agcaggcaag       12
0
     ctatttaccg atatgtgcga aggcttaccg gaaaaaagac ttcgtgggaa aacgttaatg       18
0
     tatgagttta atcactcgca tccatcagaa gttgaaaaaa gagaaagcct gattaaagaa       24
0
     atgtttgcca cggtagggga aaacgcctgg gtagaaccgc ctgtctattt ctcttacggt       30
0
     tccaacatcc atataggccg caatttttat gcaaatttca atttaaccat tgtcgatgac       36
0
     tacacggtaa caatcggtga taacgtactg attgcaccca acgttactct ttccgttacg       42
0
     ggacaccctg tacaccatga attgagaaaa aacggcgaga tgtactcttt tccgataacg       48
0
     attggcaata acgtctggat cggaagtcat gtggttatta atccaggcgt caccatcggg       54
0
     gataattctg ttattggcgc gggtagtatc gtcacaaaag acattccacc aaacgtcgtg       60
0
     gcggctggcg ttccttgtcg ggttattcgc gaaataaacg accgggataa gcactattat       66
0
     ttcaaagatt ataaagttga atcgtcagtt taaattataa aaattgcctg atacgctgcg       72
0
     cttatcaggc ctacaagttc agcgatctac attagccgca tccggcatga acaaagcgca       78
0
     ggaacaagcg tcgcatcatg cctctttgac ccacagctgc ggaaaacgta ctggtgcaaa       84
0
     acgcagggtt atgatcatca gcccaacgac gcacagcgca tgaaatgccc agtccatcag       90
0
     gtaattgccg ctgatactac gcagcacgcc agaaaaccac ggggcaagcc cggcgatgat       96
0
     aaaaccgatt ccctgcataa acgccaccag cttgccagca atagccggtt gcacagagtg      102
0
     atcgagcgcc agcagcaaac agagcggaaa cgcgccgccc agacctaacc cacacaccat      108
0
     cgcccacaat accggcaatt gcatcggcag ccagataaag ccgcagaacc ccaccagttg      114
0
     taacaccagc gccagcatta acagtttgcg ccgatcctga tggcgagcca tagcaggcat      120
0
     cagcaaagct cctgcggctt gcccaagcgt catcaatgcc agtaaggaac cgctgtactg      126
0
     cgcgctggca ccaatctcaa tatagaaagc gggtaaccag gcaatcaggc tggcgtaacc      132
0
     gccgttaatc agaccgaagt aaacacccag cgtccacgcg cggggagtga ataccacgcg      138
0
     aaccggagtg gttgttgtct tgtgggaaga ggcgacctcg cgggcgcttt gccaccacca      144
0
     ggcaaagagc gcaacaacgg caggcagcgc caccaggcga gtgtttgata ccaggtttcg      150
0
     ctatgttgaa ctaaccaggg cgttatggcg gcaccaagcc caccgccgcc catcagagcc      156
0
     gcggaccaca gccccatcac cagtggcgtg cgctgctgaa accgccgttt aatcaccgaa      162
0
     gcatcaccgc ctgaatgatg ccgatcccca ccccaccaag cagtgcgctg ctaagcagca      168
0
     gcgcactttg cgggtaaagc tcacgcatca atgcaccgac ggcaatcagc aacagactga      174
0
     tggcgacact gcgacgttcg ctgacatgct gatgaagcca gcttccggcc agcgccagcc      180
0
     cgcccatggt aaccaccggc agagcggtcg ac                                    183
2
//

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: Sat 15 Jul 2006 12:00:00
# Commandline: merger
#    -asequence tembl:eclacy
#    -bsequence tembl:eclaca
# 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



  [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
#
#
#---------------------------------------

  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 0

Known 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