
                                  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

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


% coderet 
Extract CDS, mRNA and translations from feature tables
Input sequence(s): tembl:X03487
Output sequence [hsferg1.fasta]: 

   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 
Extract CDS, mRNA and translations from feature tables
Input sequence(s): tembl:X03487
Output sequence [hsferg1.fasta]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-seqall]            seqall     Sequence database USA
  [-outseq]            seqout     Output sequence USA

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

   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

   "-outseq" associated qualifiers
   -osformat2           string     Output seq format
   -osextension2        string     File name extension
   -osname2             string     Base file name
   -osdirectory2        string     Output directory
   -osdbname2           string     Database name to add
   -ossingle2           boolean    Separate file for each entry
   -oufo2               string     UFO features
   -offormat2           string     Features format
   -ofname2             string     Features file name
   -ofdirectory2        string     Output directory

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write 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. 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 deaths


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

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   HSFERG1    standard; DNA; HUM; 512 BP.
XX
AC   X03487;
XX
SV   X03487.1
XX
DT   02-JUL-1986 (Rel. 09, Created)
DT   04-APR-1995 (Rel. 43, Last updated, Version 2)
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; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-512
RX   MEDLINE; 86120367.
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. 14:721-736(1986).
XX
DR   EPD; EP11112; HS_FRIH.
DR   SWISS-PROT; P02794; FRIH_HUMAN.
XX
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"
XX
SQ   Sequence 512 BP; 80 A; 212 C; 152 G; 64 T; 4 other;
     agnncaaacc tnagctccgc cagagcgcgc gaggcctcca gcggccgccc ctcccccaca        6
0
     gcaggggcgg ggntcccgcg cccaccggaa ggagcgggct cggggcgggc ggcgctgatt       12
0
     ggccggggcg ggcctgacgc cgacgcggct ataagagacc acaagcgacc cgcagggcca       18
0
     gacgttcttc gccgagagtc gtcggggttt cctgcttcaa cagtgcttgg acggaacccg       24
0
     gcgctcgttc cccaccccgg ccggccgccc atagccagcc ctccgtcgac ctcttcaccg       30
0
     caccctcgga ctgccccaag gcccccgccg ccgctccagc gccgcgcagc caccgccgcc       36
0
     gccgccgcct ctccttagtc gccgccatga cgaccgcgtc cacctcgcag gtgcgccaga       42
0
     actaccacca ggactcagag gccgccatca accgccagat caacctggag ctctacgcct       48
0
     cctacgttta cctgtccatg gtgagcgcgg gc                                     51
2
//

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.

  Output files for usage example

  File: hsferg1.fasta

>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

  Output files for usage example 2

  File: hsferg1.fasta

>x03487_mrna_1
cagacgttcttcgccgagagtcgtcggggtttcctgcttcaacagtgcttggacggaacc
cggcgctcgttccccaccccggccggccgcccatagccagccctccgtcgacctcttcac
cgcaccctcggactgccccaaggcccccgccgccgctccagcgccgcgcagccaccgccg
ccgccgccgcctctccttagtcgccgccatgacgaccgcgtccacctcgcaggtgcgcca
gaactaccaccaggactcagaggccgccatcaaccgccagatcaacctggagctctacgc
ctcctacgtttacctgtccatg

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
   sixpack      Display a DNA sequence with 6-frame translation and ORFs
   transeq      Translate nucleic acid sequences
   twofeat      Finds neighbouring pairs of features in sequences

Author(s)

   Alan Bleasby (ableasby © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, 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
