                                  tranalign



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Function

   Generate an alignment of nucleic coding regions from aligned proteins

Description

   tranalign is a re-implementation in EMBOSS of the program mrtrans by
   Bill Pearson. It reads a set of (unaligned) nucleotide sequences and a
   corresponding set of aligned protein sequences which are the
   translations, and writes the coding regions to file as a nucleotide
   sequence alignment. The sequences must be in the same order in the
   input sets. Each nucleotide sequence is translated in all three forward
   frames using the specified genetic code and the translations compared
   to the corresponding protein sequence from input the alignment. The
   contiguous nucleotide sequence that coded the protein is written to
   file (it will not splice together different exons to produce a coding
   sequence).

Algorithm

   The protein sequences will typically include gap (-) characters. These
   are ignored during sequence comparison but replaced by --- in the
   nucleotide sequence alignment output.

Usage

   Here is a sample session with tranalign


% tranalign ../data/tranalign.pep tranalign2.seq
Generate an alignment of nucleic coding regions from aligned proteins


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Generate an alignment of nucleic coding regions from aligned proteins
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-asequence]         seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
  [-bsequence]         seqset     (Aligned) protein sequence set filename and
                                  optional format, or reference (input USA)
  [-outseq]            seqoutset  [.] (Aligned) nucleotide
                                  sequence set filename and optional format
                                  (output USA)

   Additional (Optional) qualifiers:
   -table              menu       [0] Code to use (Values: 0 (Standard); 1
                                  (Standard (with alternative initiation
                                  codons)); 2 (Vertebrate Mitochondrial); 3
                                  (Yeast Mitochondrial); 4 (Mold, Protozoan,
                                  Coelenterate Mitochondrial and
                                  Mycoplasma/Spiroplasma); 5 (Invertebrate
                                  Mitochondrial); 6 (Ciliate Macronuclear and
                                  Dasycladacean); 9 (Echinoderm
                                  Mitochondrial); 10 (Euplotid Nuclear); 11
                                  (Bacterial); 12 (Alternative Yeast Nuclear);
                                  13 (Ascidian Mitochondrial); 14 (Flatworm
                                  Mitochondrial); 15 (Blepharisma
                                  Macronuclear); 16 (Chlorophycean
                                  Mitochondrial); 21 (Trematode
                                  Mitochondrial); 22 (Scenedesmus obliquus);
                                  23 (Thraustochytrium Mitochondrial))

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-asequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each 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
   -scircular1         boolean    Sequence is circular
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 each sequence to be used
   -send2              integer    End of each 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
   -scircular2         boolean    Sequence is circular
   -sformat2           string     Input sequence format
   -iquery2            string     Input query fields or ID list
   -ioffset2           integer    Input start position offset
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         string     Features file name

   "-outseq" associated qualifiers
   -osformat3          string     Output seq format
   -osextension3       string     File name extension
   -osname3            string     Base file name
   -osdirectory3       string     Output directory
   -osdbname3          string     Database name to add
   -ossingle3          boolean    Separate file for each entry
   -oufo3              string     UFO features
   -offormat3          string     Features format
   -ofname3            string     Features file name
   -ofdirectory3       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


Input file format

   The input is a set of unaligned nucleic sequences and the set of
   aligned protein sequences to be used as a guide in the alignment of the
   output nucleic sequences.

   The ID names of the nucleic acid and protein sequences are NOT checked
   to see if they correspond to each other. They can have any names.

   There must be at least as many protein sequences as nucleic acid
   sequence - extra protein sequences are ignored.

   Each of the nucleic acid sequences must have a corresponding protein
   sequence which is derived from the coding region of that nucleic acid
   sequence. The two sets of sequences must be in the same order.

  Input files for usage example

  File: tranalign.seq

>HSFAU1
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggccccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa
>HSFAU2
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

   In general, it is better to use protein sequences for multiple
   alignment, but to use DNA sequences for phylogeny, for example, when
   using the programs dnadist, dnapars, dnaml, etc in the PHYLIP package.
   Where one has a protein sequence alignment, it would be time consuming
   to remove gap characters before back-translating the proteins.
   tranalign helps by generating aligned cDNA sequences from a protein
   sequence alignment.

   tranalign finds the coding regions for contiguous sequences only. It
   will not splice together different exons to produce a coding sequence.
   You should therefore use either mRNA sequences, or nucleic sequences
   which you have constructed to hold a contiguous coding region (maybe
   using extractseq or yank and union?).

References

   None.

Warnings

   The sequences must be in the same order in both input sets of
   sequences. Some alignment program (including clustalw/emma) will
   re-order their input sequences so as to group similar sequences
   together.

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 sequence alignment (ClustalW wrapper)
                    infoalign    Display basic information about a multiple sequence alignment
                    plotcon      Plot conservation of a sequence alignment
                    prettyplot   Draw a sequence alignment with pretty formatting
                    showalign    Display a multiple sequence alignment in pretty format

Author(s)

                    The original program mrtrans was written by Bill Pearson
                    (wrp@virginia.edu)

                    tranalign was written in EMBOSS code using the description of mrtrans
                    as a guide by 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 (c) emboss.open-bio.org) not to the original author.

History

                    mrtrans written (Jan 1991, July 1987) - Bill Pearson

                    tranalign written (March 2002) - Gary Williams

Target users

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

Comments

                    None
