
                              EMBOSS: coderet
     _________________________________________________________________
   
                                Program coderet
                                       
Function

   Extract CDS, mRNA and translations from feature tables
   
Description

   The feature table of sequence database entries often have sections
   like this:
   
   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)
     _________________________________________________________________
   
   or:
   
   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)
     _________________________________________________________________
   
   or:
   
   This specifies that the translation of the coding region is as
   follows.
     _________________________________________________________________
   
FT                   /translation="MAQDSVDLSCDYQFWMQKLSVWDQASTLETQQDTCLHVAQFQEF
L
FT                   RKMYEALKEMDSNTVIERFPTIGQLLAKACWNPFILAYDESQKILIWCLCCLINKEPQ
N
FT                   SGQSKLNSWIQGVLSHILSALRFDKEVALFTQGLGYAPIDYYPGLLKNMVLSLASELR
E
FT                   NHLNGFNTQRRMAPERVASLSRVCVPLITLTDVDPLVEALLICHGREPQEILQPEFFE
A
FT                   VNEAILLKKISLPMSAVVCLWLRHLPSLEKAMLHLFEKLISSERNCLRRIECFIKDSS
L
FT                   PQAACHPAIFRVDEMFRCALLETDGALEIIATIQVFTQCFVEALEKASKQLRFALKTY
F
FT                   PYTSPSLAMVLLQDPQDIPRGHWLQTLKHISELLREAVEDQTHGSCGGPFESWFLFIH
F
FT                   GGWAEMVAEQLLMSAAEPPTALLWLLAFYYGPRDGRQQRAQTMVQVKAVLGHLLAMSR
S
FT                   SSLSAQDLQTVAGQGTDTDLRAPAQQLIRHLLLNFLLWAPGGHTIAWDVITLMAHTAE
I
FT                   THEIIGFLDQTLYRWNRLGIESPRSEKLARELLKELRTQV"
     _________________________________________________________________
   
   It is often a tedious and error-prone job to extract the several
   sections of these sequences from the database entries and to join them
   together to construct the indicated finished sequence.
   
   coderet does this job for you.
   
   You specify the sequence containing the feature table and it extracts
   the required CDS, mRNA and/or protein sequences specified by this
   feature table. If any sequences are in other entries of that database,
   they are automatically fetched and incorporated correctly into the
   final sequence.
   
   The translations are not made from the coding sequence, they are
   extracted directly from the translation sequence held in the feature
   table.
   
Usage

   Here is a sample session with coderet:
   
   The EMBL sequence X03487's feature table is as follows:
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FH   Key             Location/Qualifiers
FH
FT   source          1..512
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
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                   /db_xref="SWISS-PROT:P02794"
FT                   /label=apoh_cds
FT                   /product="apoferritin H subunit"
FT                   /protein_id="CAA27205.1"
FT                   /translation="MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDR
D
FT                   DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMEC
A
FT                   LHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAP
E
FT                   SGLAEYLFDKHTLGDSDNES"
FT   intron          501..>512
FT                   /note="intron I"
     _________________________________________________________________
   
   This means that the mRNA sequence is from position 179 to 500 in this
   sequence.
   The coding sequence is formed by joining the region from 387 to 500 in
   this sequence together with regions from two other entries in this
   database: X03488 and X03488.
   The translation of the coding sequence is also given.
   
   To extract all of the CDS, mRNA and the protein translations, type:
   
% coderet
Extract CDS, mRNA and translations from feature tables
Input sequence(s): embl:X03487
Output sequence [hsferg1.fasta]:

   The result is as follows:
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>x03487_cds_1
atgacgaccgcgtccacctcgcaggtgcgccagaactaccaccaggactcagaggccgcc
atcaaccgccagatcaacctggagctctacgcctcctacgtttacctgtccatgtcttac
tactttgaccgcgatgatgtggctttgaagaactttgccaaatactttcttcaccaatct
catgaggagagggaacatgctgagaaactgatgaagctgcagaaccaacgaggtggccga
atcttccttcaggatatcaagaaaccagactgtgatgactgggagagcgggctgaatgca
atggagtgtgcattacatttggaaaaaaatgtgaatcagtcactactggaactgcacaaa
ctggccactgacaaaaatgacccccatttgtgtgacttcattgagacacattacctgaat
gagcaggtgaaagccatcaaagaattgggtgaccacgtgaccaacttgcgcaagatggga
gcgcccgaatctggcttggcggaatatctctttgacaagcacaccctgggagacagtgat
aatgaaagctaa
>x03487_mrna_1
cagacgttcttcgccgagagtcgtcggggtttcctgcttcaacagtgcttggacggaacc
cggcgctcgttccccaccccggccggccgcccatagccagccctccgtcgacctcttcac
cgcaccctcggactgccccaaggcccccgccgccgctccagcgccgcgcagccaccgccg
ccgccgccgcctctccttagtcgccgccatgacgaccgcgtccacctcgcaggtgcgcca
gaactaccaccaggactcagaggccgccatcaaccgccagatcaacctggagctctacgc
ctcctacgtttacctgtccatg
>x03487_pro_1
MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS
HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHK
LATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSD
NES
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   Note that there is a mixture of nucleic and protein sequences in this
   file
   
   To only extract the mRNA sequence, type:
   
% coderet -nocds -notranslation
Extract CDS, mRNA and translations from feature tables
Input sequence(s): embl:X03487
Output sequence [hsferg1.fasta]:

Command line arguments

   Mandatory qualifiers:
  [-seqall]            seqall     Sequence database USA
  [-seqout]            seqout     Output sequence USA

   Optional qualifiers: (none)
   Advanced qualifiers:
   -[no]cds            bool       Extract CDS sequences
   -[no]mrna           bool       Extract mrna sequences
   -[no]translation    bool       Extract translated sequences

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-seqall]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-seqout]
   (Parameter 2) Output sequence USA Writeable sequence <sequence>.format
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -[no]cds Extract CDS sequences Yes/No Yes
   -[no]mrna Extract mrna sequences Yes/No Yes
   -[no]translation Extract translated sequences Yes/No Yes
   
Input file format

   USA of one or more nucleic sequences having CDS, mRNA or translation
   headings in their feature tables.
   
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
   'HSXYZ' would be named 'HSXYZ_cds_2'.
   
   The translations are not made from the coding sequence, they are
   extracted directly from the translation sequence held in the feature
   table.
   
Data files

   None.
   
Notes

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

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name                          Description
   backtranseq  Back translate a protein sequence
   extractfeat  Extract features from a sequence
   maskfeat     Mask off features of a sequence
   plotorf      Plot potential open reading frames
   prettyseq    Output sequence with translated ranges
   remap        Display a sequence with restriction cut sites, translation etc
   showfeat     Show features of a sequence
   showorf      Pretty output of DNA translations
   showseq      Display a sequence with features, translation etc
   swissparse   Retrieves sequences from swissprot using keyword search
   transeq      Translate nucleic acid sequences
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.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
