                                   coderet



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Function

   Extract CDS, mRNA and translations from feature tables

Description

   coderet extracts the coding nucleotide sequence (CDS), messenger RNA
   nucleotide sequence (mRNA) and translations specified by the feature
   tables of the input sequence(s). If the sequences to be extracted are
   in other entries of that database, they are automatically fetched and
   incorporated correctly into the output.

   For each input sequence, an output sequence file is written containing
   any CDS, mRNA and protein translation sequences from the input feature
   table. Optionally, the CDS, mRNA, translated protein sequence and
   non-coding nucleotide sequence regions may be written to separate
   files.

Usage

   Here is a sample session with coderet

   To extract all of the CDS, mRNA, non-coding and the protein
   translations:


% coderet
Extract CDS, mRNA and translations from feature tables
Input nucleotide sequence(s): tembl:x03487
Output file [x03487.coderet]:
Coding nucleotide output sequence(s) (optional) [x03487.cds]:
Messenger RNA nucleotide output sequence(s) (optional) [x03487.mrna]:
Translated coding protein output sequence(s) (optional) [x03487.prot]:
Non-coding nucleotide output sequence(s) (optional) [x03487.noncoding]:


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

   Example 2

   To only extract the mRNA sequence:


% coderet -nocds -notranslation -norest
Extract CDS, mRNA and translations from feature tables
Input nucleotide sequence(s): tembl:X03487
Output file [x03487.coderet]:
Messenger RNA nucleotide output sequence(s) (optional) [x03487.mrna]:


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

Command line arguments

Extract CDS, mRNA and translations from feature tables
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-seqall]            seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outfile]           outfile    [*.coderet] Output file name
  [-cdsoutseq]         seqoutall  [.] Coding nucleotide
                                  output sequence(s) (optional)
  [-mrnaoutseq]        seqoutall  [.] Messenger RNA
                                  nucleotide output sequence(s) (optional)
  [-translationoutseq] seqoutall  [.] Translated coding
                                  protein output sequence(s) (optional)
  [-restoutseq]        seqoutall  [.] Non-coding nucleotide
                                  output sequence(s) (optional)

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

   "-seqall" 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
   -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

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   "-cdsoutseq" 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

   "-mrnaoutseq" 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

   "-translationoutseq" associated qualifiers
   -osformat5          string     Output seq format
   -osextension5       string     File name extension
   -osname5            string     Base file name
   -osdirectory5       string     Output directory
   -osdbname5          string     Database name to add
   -ossingle5          boolean    Separate file for each entry
   -oufo5              string     UFO features
   -offormat5          string     Features format
   -ofname5            string     Features file name
   -ofdirectory5       string     Output directory

   "-restoutseq" associated qualifiers
   -osformat6          string     Output seq format
   -osextension6       string     File name extension
   -osname6            string     Base file name
   -osdirectory6       string     Output directory
   -osdbname6          string     Database name to add
   -ossingle6          boolean    Separate file for each entry
   -oufo6              string     UFO features
   -offormat6          string     Features format
   -ofname6            string     Features file name
   -ofdirectory6       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

   coderet reads one or more nucleic sequence USAs having CDS, mRNA or
   translation headings in their feature tables.

  Input files for usage example

   'tembl:x03487' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:x03487

ID   X03487; SV 1; linear; genomic DNA; STD; HUM; 512 BP.
XX
AC   X03487;
XX
DT   02-JUL-1986 (Rel. 09, Created)
DT   24-AUG-2005 (Rel. 84, Last updated, Version 3)
XX
DE   Human apoferritin H gene exon 1
XX
KW   ferritin.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-512
RX   DOI; 10.1093/nar/14.2.721.
RX   PUBMED; 3003694.
RA   Costanzo F., Colombo M., Staempfli S., Santoro C., Marone M., Frank R.,
RA   Delius H., Cortese R.;
RT   "Structure of gene and pseudogenes of human apoferritin H";
RL   Nucleic Acids Res. 14(2):721-736(1986).
XX
DR   EPD; EP11112; HS_FTH1.
DR   RFAM; RF00037; IRE.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..512
FT                   /organism="Homo sapiens"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:9606"
FT   misc_feature    65..70
FT                   /note="GGGCGG box"
FT   misc_feature    103..108
FT                   /note="GGGCGG box"
FT   misc_feature    126..131
FT                   /note="GGGCGG box"
FT   promoter        150..154
FT                   /note="put. TATA box"
FT   mRNA            179..500
FT                   /note="exon 1"
FT   CDS             join(387..500,X03488.1:50..196,X03488.1:453..578,
FT                   X03488.1:674..838)
FT                   /product="apoferritin H subunit"
FT                   /db_xref="GDB:120617"
FT                   /db_xref="GOA:P02794"
FT                   /db_xref="HGNC:3976"
FT                   /db_xref="InterPro:IPR014034"
FT                   /db_xref="PDB:3ES3"
FT                   /db_xref="UniProtKB/Swiss-Prot:P02794"
FT                   /protein_id="CAA27205.1"
FT                   /translation="MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRD
FT                   DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECA
FT                   LHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPE
FT                   SGLAEYLFDKHTLGDSDNES"
FT   intron          501..>512
FT                   /note="intron I"
XX
SQ   Sequence 512 BP; 80 A; 212 C; 152 G; 64 T; 4 other;
     agnncaaacc tnagctccgc cagagcgcgc gaggcctcca gcggccgccc ctcccccaca        60
     gcaggggcgg ggntcccgcg cccaccggaa ggagcgggct cggggcgggc ggcgctgatt       120
     ggccggggcg ggcctgacgc cgacgcggct ataagagacc acaagcgacc cgcagggcca       180
     gacgttcttc gccgagagtc gtcggggttt cctgcttcaa cagtgcttgg acggaacccg       240
     gcgctcgttc cccaccccgg ccggccgccc atagccagcc ctccgtcgac ctcttcaccg       300
     caccctcgga ctgccccaag gcccccgccg ccgctccagc gccgcgcagc caccgccgcc       360
     gccgccgcct ctccttagtc gccgccatga cgaccgcgtc cacctcgcag gtgcgccaga       420
     actaccacca ggactcagag gccgccatca accgccagat caacctggag ctctacgcct       480
     cctacgttta cctgtccatg gtgagcgcgg gc                                     512
//

  Input files for usage example 2

  Database entry: tembl:X03487

ID   X03487; SV 1; linear; genomic DNA; STD; HUM; 512 BP.
XX
AC   X03487;
XX
DT   02-JUL-1986 (Rel. 09, Created)
DT   24-AUG-2005 (Rel. 84, Last updated, Version 3)
XX
DE   Human apoferritin H gene exon 1
XX
KW   ferritin.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-512
RX   DOI; 10.1093/nar/14.2.721.
RX   PUBMED; 3003694.
RA   Costanzo F., Colombo M., Staempfli S., Santoro C., Marone M., Frank R.,
RA   Delius H., Cortese R.;
RT   "Structure of gene and pseudogenes of human apoferritin H";
RL   Nucleic Acids Res. 14(2):721-736(1986).
XX
DR   EPD; EP11112; HS_FTH1.
DR   RFAM; RF00037; IRE.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..512
FT                   /organism="Homo sapiens"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:9606"
FT   misc_feature    65..70
FT                   /note="GGGCGG box"
FT   misc_feature    103..108
FT                   /note="GGGCGG box"
FT   misc_feature    126..131
FT                   /note="GGGCGG box"
FT   promoter        150..154
FT                   /note="put. TATA box"
FT   mRNA            179..500
FT                   /note="exon 1"
FT   CDS             join(387..500,X03488.1:50..196,X03488.1:453..578,
FT                   X03488.1:674..838)
FT                   /product="apoferritin H subunit"
FT                   /db_xref="GDB:120617"
FT                   /db_xref="GOA:P02794"
FT                   /db_xref="HGNC:3976"
FT                   /db_xref="InterPro:IPR014034"
FT                   /db_xref="PDB:3ES3"
FT                   /db_xref="UniProtKB/Swiss-Prot:P02794"
FT                   /protein_id="CAA27205.1"
FT                   /translation="MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRD
FT                   DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECA
FT                   LHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPE
FT                   SGLAEYLFDKHTLGDSDNES"
FT   intron          501..>512
FT                   /note="intron I"
XX
SQ   Sequence 512 BP; 80 A; 212 C; 152 G; 64 T; 4 other;
     agnncaaacc tnagctccgc cagagcgcgc gaggcctcca gcggccgccc ctcccccaca        60
     gcaggggcgg ggntcccgcg cccaccggaa ggagcgggct cggggcgggc ggcgctgatt       120
     ggccggggcg ggcctgacgc cgacgcggct ataagagacc acaagcgacc cgcagggcca       180
     gacgttcttc gccgagagtc gtcggggttt cctgcttcaa cagtgcttgg acggaacccg       240
     gcgctcgttc cccaccccgg ccggccgccc atagccagcc ctccgtcgac ctcttcaccg       300
     caccctcgga ctgccccaag gcccccgccg ccgctccagc gccgcgcagc caccgccgcc       360
     gccgccgcct ctccttagtc gccgccatga cgaccgcgtc cacctcgcag gtgcgccaga       420
     actaccacca ggactcagag gccgccatca accgccagat caacctggag ctctacgcct       480
     cctacgttta cctgtccatg gtgagcgcgg gc                                     512
//

Output file format

   The output is a sequence file containing any CDS, mRNA and protein
   translation sequences as specified by the feature table of the
   sequence(s).

   One or more of CDS, mRNA, translation can be excluded from the output
   by using the appropriate qualifiers to the program (i.e. -nocds, etc.)

   The ID names of the output sequences are constructed from the name of
   the input sequence, the type of feature being output (i.e. cds, mrna,
   pro) and a unique ordinal number for this type to distinguish it from
   others in this sequence. The name, type and number of separated by
   underscore characters. Thus the second CDS feature in the sequence
   'A12345' would be named 'A12345_cds_2'.

   The translations are not made from the coding sequence, they are
   extracted directly from the translation sequence held in the feature
   table.

  Output files for usage example

  File: x03487.cds

>x03487_cds_1
atgacgaccgcgtccacctcgcaggtgcgccagaactaccaccaggactcagaggccgcc
atcaaccgccagatcaacctggagctctacgcctcctacgtttacctgtccatgtcttac
tactttgaccgcgatgatgtggctttgaagaactttgccaaatactttcttcaccaatct
catgaggagagggaacatgctgagaaactgatgaagctgcagaaccaacgaggtggccga
atcttccttcaggatatcaagaaaccagactgtgatgactgggagagcgggctgaatgca
atggagtgtgcattacatttggaaaaaaatgtgaatcagtcactactggaactgcacaaa
ctggccactgacaaaaatgacccccatttgtgtgacttcattgagacacattacctgaat
gagcaggtgaaagccatcaaagaattgggtgaccacgtgaccaacttgcgcaagatggga
gcgcccgaatctggcttggcggaatatctctttgacaagcacaccctgggagacagtgat
aatgaaagctaa

  File: x03487.mrna

>x03487_mrna_1
cagacgttcttcgccgagagtcgtcggggtttcctgcttcaacagtgcttggacggaacc
cggcgctcgttccccaccccggccggccgcccatagccagccctccgtcgacctcttcac
cgcaccctcggactgccccaaggcccccgccgccgctccagcgccgcgcagccaccgccg
ccgccgccgcctctccttagtcgccgccatgacgaccgcgtccacctcgcaggtgcgcca
gaactaccaccaggactcagaggccgccatcaaccgccagatcaacctggagctctacgc
ctcctacgtttacctgtccatg

  File: x03487.prot

>x03487_pro_1
MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS
HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHK
LATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSD
NES

  File: x03487.noncoding

>x03487_noncoding_1
agnncaaacctnagctccgccagagcgcgcgaggcctccagcggccgcccctcccccaca
gcaggggcggggntcccgcgcccaccggaaggagcgggctcggggcgggcggcgctgatt
ggccggggcgggcctgacgccgacgcggctataagagaccacaagcgacccgcagggc
>x03487_noncoding_501
gtgagcgcgggc

  File: x03487.coderet

   CDS  mRNA non-c Trans Total Sequence
 ===== ===== ===== ===== ===== ========
     1     1     6     1     8 X03487

  Output files for usage example 2

  File: x03487.coderet

  mRNA Total Sequence
 ===== ===== ========
     1     1 X03487

Data files

   None.

Notes

   One or more of CDS, mRNA, translation or non-coding regions can be
   excluded from output with the appropriate qualifiers; "no" is prepended
   to the qualifier name, for example -nocds would exclude the coding
   sequence.

   The translations are not made from the coding sequence, they are
   extracted directly from the translation sequence held in the feature
   table.

   The regions of the feature table that concern us are shown below.

   This specifies that the coding sequence for the gene is constructed by
   joining several sections of code, many of which are in other entries in
   this database:
FT   CDS             join(U21925.1:818..987,U21926.1:258..420,
FT                   U21927.1:428..520,U21928.1:196..336,U21929.1:279..415,
FT                   U21930.1:895..1014,516..708)

   This specifies that the messenger RNA sequence for the gene is
   constructed by joining several sections of code, many of which are in
   other entries in this database.
FT   mRNA            join(M88628.1:1006..1318,M88629.1:221..342,
FT                   M88630.1:101..223,M88631.1:46..258,M88632.1:104..172,
FT                   M88633.1:387..503,M88634.1:51..272,M88635.1:303..564,
FT                   M88635.1:849..1020,M88636.1:282..375,M88637.1:39..253,
FT                   M88638.1:91..241,M88639.1:168..377,M88640.1:627..3732,
FT                   M88641.1:158..311,M88642.1:1051..1263,M88642.1:1550..1778,
FT                   M88642.1:1986..2168,M88642.1:3904..4020,
FT                   M88642.1:4627..4698,M88643.1:39..124,M88644.1:42..197,
FT                   M88645.1:542..686,M88646.1:75..223,M88647.1:109..285,
FT                   253..2211)

   This specifies that the translation of the coding region is as follows:
FT                   /translation="MAQDSVDLSCDYQFWMQKLSVWDQASTLETQQDTCLHVAQFQEFL
FT                   RKMYEALKEMDSNTVIERFPTIGQLLAKACWNPFILAYDESQKILIWCLCCLINKEPQN
FT                   SGQSKLNSWIQGVLSHILSALRFDKEVALFTQGLGYAPIDYYPGLLKNMVLSLASELRE
FT                   NHLNGFNTQRRMAPERVASLSRVCVPLITLTDVDPLVEALLICHGREPQEILQPEFFEA
FT                   VNEAILLKKISLPMSAVVCLWLRHLPSLEKAMLHLFEKLISSERNCLRRIECFIKDSSL
FT                   PQAACHPAIFRVDEMFRCALLETDGALEIIATIQVFTQCFVEALEKASKQLRFALKTYF
FT                   PYTSPSLAMVLLQDPQDIPRGHWLQTLKHISELLREAVEDQTHGSCGGPFESWFLFIHF
FT                   GGWAEMVAEQLLMSAAEPPTALLWLLAFYYGPRDGRQQRAQTMVQVKAVLGHLLAMSRS
FT                   SSLSAQDLQTVAGQGTDTDLRAPAQQLIRHLLLNFLLWAPGGHTIAWDVITLMAHTAEI
FT                   THEIIGFLDQTLYRWNRLGIESPRSEKLARELLKELRTQV"

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   backtranambig    Back-translate a protein sequence to ambiguous nucleotide
                    sequence
   backtranseq      Back-translate a protein sequence to a nucleotide sequence
   extractfeat      Extract features from sequence(s)
   maskfeat         Write a sequence with masked features
   plotorf          Plot potential open reading frames in a nucleotide sequence
   prettyseq        Write a nucleotide sequence and its translation to file
   remap            Display restriction enzyme binding sites in a nucleotide sequence
   showfeat         Display features of a sequence in pretty format
   showorf          Display a nucleotide sequence and translation in pretty format
   showseq          Displays sequences with features in pretty format
   sixpack          Display a DNA sequence with 6-frame translation and ORFs
   transeq          Translate nucleic acid sequences
   twofeat          Finds neighbouring pairs of features in sequence(s)

Author(s)

   Alan Bleasby (ajb (c) ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

   Written (Nov 2000) - Alan Bleasby.

Target users

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

Comments

   None
