tranalign.txt

emboss的linux版本的源代码

ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa
>HSFAU3
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa
>HSFAU4
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa
>HSFAU5
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtaggccgcatgctttttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa

  File: tranalign.pep

>HSFAU1_3
PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVAS-LEGIAPEDQVV
LLAG-PLEDEATLGQCGVEALTTLEVAGRMLG-GKVHGSLARAGKVRGQTPKVAKQEKKK
KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS
>HSFAU2_3
PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVAS-LEGIAPEDQVV
LLAGAPLEDALWASAGWRP
>HSFAU3_3
PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVAS-LEGIAPEDQVV
LLAGAPLEDEATLGQCGVEALTTLEVAGRMLG-GKVHGSLARAGKVRGQTPKGAKQEKKK
KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS
>HSFAU4_3
PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHEIASLEGIAPEDQVV
LLAGAPLEDEATLGQCGVEALTTLEVAGRMLARGKVHGSLARAGKVRGQTPKVAKQEKKK
KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS
>HSFAU5_3
PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVAS-LEGIAPEDQVV
LLAGAPLEDEATLGQCGVEALTTLEVGRMLFG-GKVHGSLARAGKVRGQTPKVAKQEKKK
KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS

Output file format

  Output files for usage example

  File: tranalign2.seq

>HSFAU1
cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
ctcctggcaggc---cccctggaggatgaggccactctgggccagtgcggggtggaggcc
ctgactaccctggaagtagcaggccgcatgcttgga---ggtaaagttcatggttccctg
gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
cccacctttggcaagaagaagggccccaatgccaactct
>HSFAU2
cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
ctcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc---
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
---------------------------------------
>HSFAU3
cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc
ctgactaccctggaagtagcaggccgcatgcttgga---ggtaaagttcatggttccctg
gcccgtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaag
aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
cccacctttggcaagaagaagggccccaatgccaactct
>HSFAU4
cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
cagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtg
ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc
ctgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctg
gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
cccacctttggcaagaagaagggccccaatgccaactct
>HSFAU5
cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc
ctgactaccctggaagtaggccgcatgctttttgga---ggtaaagttcatggttccctg
gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
cccacctttggcaagaagaagggccccaatgccaactct

   The output is the regions of the nucleic acid sequences which code for
   the corresponding protein sequence, with gap characters ('-')
   introduced so that they have the same alignment as the corresponding
   protein sequences.

Data files

   None.

Notes

   The sequences must be in the same order in both sets of sequences. A
   common problem you should be aware of is that some alignment program
   (including clustalw/emma) will re-order the aligned sequences to group
   similar sequences together.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   "No guide protein sequence available for nucleic sequence xxx" - the
   corresponding protein sequence for this nucleic sequence has not been
   input. You have input more nucleic acid sequences than protein
   sequences.

   "Guide protein sequence xxx not found in nucleic sequence xxx" - the
   region of the nucleic sequence which codes for the protein was not
   found. The coding region in the nucleic acid sequence must be a single
   contiguous sequence. The protein sequence might not be the
   corresponding one for this nucleic acid sequence if they are out of
   order.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                        Description
   edialign     Local multiple alignment of sequences
   emma         Multiple alignment program - interface to ClustalW program
   infoalign    Information on a multiple sequence alignment
   plotcon      Plot quality of conservation of a sequence alignment
   prettyplot   Displays aligned sequences, with colouring and boxing
   showalign    Displays a multiple sequence alignment

Author(s)

   The original program mrtrans was written by Bill Pearson
   ([e-mail])

   tranalign was written in EMBOSS code using the description of mrtrans
   as a guide by Gary Williams (gwilliam