coderet.txt

emboss的linux版本的源代码

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.cds

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

  File: hsferg1.mrna

>x03487_mrna_1
cagacgttcttcgccgagagtcgtcggggtttcctgcttcaacagtgcttggacggaacc
cggcgctcgttccccaccccggccggccgcccatagccagccctccgtcgacctcttcac
cgcaccctcggactgccccaaggcccccgccgccgctccagcgccgcgcagccaccgccg
ccgccgccgcctctccttagtcgccgccatgacgaccgcgtccacctcgcaggtgcgcca
gaactaccaccaggactcagaggccgccatcaaccgccagatcaacctggagctctacgc
ctcctacgtttacctgtccatg

  File: hsferg1.prot

>x03487_pro_1
MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS
HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHK
LATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSD
NES

  File: hsferg1.noncoding

>x03487_noncoding_1
agnncaaacctnagctccgccagagcgcgcgaggcctccagcggccgcccctcccccaca
gcaggggcggggntcccgcgcccaccggaaggagcgggctcggggcgggcggcgctgatt
ggccggggcgggcctgacgccgacgcggctataagagaccacaagcgacccgcagggc
>x03487_noncoding_501
gtgagcgcgggc

  File: hsferg1.coderet

   CDS  mRNA non-c Trans Total Sequence
 ===== ===== ===== ===== ===== ========
     1     1     2     1     5 HSFERG1

  Output files for usage example 2

  File: hsferg1.coderet

  mRNA Total Sequence
 ===== ===== ========
     1     1 HSFERG1

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
   backtranambig Back translate a protein sequence to ambiguous codons
   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 sequence with restriction 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 (ajb