getorf.txt

emboss的linux版本的源代码

     caaatgctga atgagggcat cgttcccact gcgatgctgg ttgccaacga tcagatggcg       78
0
     ctgggcgcaa tgcgcgccat taccgagtcc gggctgcgcg ttggtgcgga tatctcggta       84
0
     gtgggatacg acgataccga agacagctca tgttatatcc cgccgtcaac caccatcaaa       90
0
     caggattttc gcctgctggg gcaaaccagc gtggaccgct tgctgcaact ctctcagggc       96
0
     caggcggtga agggcaatca gctgttgccc gtctcactgg tgaaaagaaa aaccaccctg      102
0
     gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat gcagctggca      108
0
     cgacaggttt cccgactgga aagcgggcag tga                                   111
3
//

Output file format

   The output is a sequence file containing predicted open reading frames
   longer than the minimum size, which defaults to 30 bases (i.e. 10
   amino acids).

  Output files for usage example

  File: eclaci.orf

>ECLACI_1 [735 - 1112] E. coli laci gene (codes for the lac repressor).
GHRSHCDAGCQRSDGAGRNARHYRVRAARWCGYLGSGIRRYRRQLMLYPAVNHHQTGFSP
AGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFP
TGKRAV
>ECLACI_2 [1 - 1110] E. coli laci gene (codes for the lac repressor).
PEESQFRVVNVKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPN
RVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAA
VHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLG
VEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTM
QMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIK
QDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLA
RQVSRLESGQ*
>ECLACI_3 [465 - 49] (REVERSE SENSE) E. coli laci gene (codes for the lac repre
ssor).
RRNISAGSFHSNGILVIQRIVNDQPTDALREKIVHRRFTGFDAASFYHRHHHAGTQLIGA
RFNRRDNLRRRVQGQTGGGNANQQRLFARQLLCHAVGNVIQLRHRRFHFFPRFRRNVAGL
VHHAGNGLIRDTGILCDIV

   The name of the ORF sequences is constructed from the name of the
   input sequence with an underscore character ('_') and a unique ordinal
   number of the ORF found appended. The description of the output ORF
   sequence is constructed from the description of the input sequence
   with the start and end positions of the ORF prepended.

   The unique number appended to the name is simply used to create new
   unique sequence names, it does not imply any further information
   indicating any order, positioning or sense-strand of the ORFs.

   If the ORF has been found in the reverse sense, then the start
   position will be smaller than the end position. The numbering uses the
   forward-sense positions, but read in the reverse sense. For example,
   >ECLACI_3 [465 - 49] in the output above is a reverse-sense ORF
   running from position 465 to 49. The description will also contain
   '(REVERSE SENSE)'.

   If the sequence has been specified as a circular genome (using the
   command-line switch '-circular'), then ORFs can potentially continue
   past the 'end' of the input sequence (the breakpoint of the circular
   genome) and into the 'start' of the sequence again. This is dealt with
   by appending the sequence to itself three times and reporting long
   ORFs that are found in this extended sequence. Any ORF that is longer
   that three times the sequence length (i.e one that continues without
   hitting a STOP at any point in the genome) will be reported as being a
   maximum of three times the length of the input sequence. Note that the
   end position of an ORF in circular genomes can be apparently longer
   than the input sequence if the ORF crosses the breakpoint. If the ORF
   crosses the breakpoint, then the text '(ORF crosses the breakpoint)'
   will be added to the description of the output sequence.

Data files

   The START and STOP codons used by getorf are defined in the Genetic
   Code data files. By default, Genetic Code file EGC.0 is used.

   The default file EGC.0 is the 'Standard Code' with the rarely used
   alternate START codons omitted, it only has the normal 'AUG' START
   codon. The 'Standard Code' with the rarely used alternate START codons
   included is Genetic Code file EGC.1.

   It is expected that user will sometimes wish to customise a Genetic
   Code file. To do this, use the program embossdata.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

   The Genetic Code data files are based on the NCBI genetic code tables.
   Their names and descriptions are:

   EGC.0
          Standard (Differs from GC.1 in that it only has initiation site
          'AUG')

   EGC.1
          Standard

   EGC.2
          Vertebrate Mitochodrial

   EGC.3
          Yeast Mitochondrial

   EGC.4
          Mold, Protozoan, Coelenterate Mitochondrial and
          Mycoplasma/Spiroplasma

   EGC.5
          Invertebrate Mitochondrial

   EGC.6
          Ciliate Macronuclear and Dasycladacean

   EGC.9
          Echinoderm Mitochondrial

   EGC.10
          Euplotid Nuclear

   EGC.11
          Bacterial

   EGC.12
          Alternative Yeast Nuclear

   EGC.13
          Ascidian Mitochondrial

   EGC.14
          Flatworm Mitochondrial

   EGC.15
          Blepharisma Macronuclear

   EGC.16
          Chlorophycean Mitochondrial

   EGC.21
          Trematode Mitochondrial

   EGC.22
          Scenedesmus obliquus

   EGC.23
          Thraustochytrium Mitochondrial

   The format of these files is very simple.

   It consists of several lines of optional comments, each starting with
   a '#' character.

   These are followed the line: 'Genetic Code [n]', where 'n' is the
   number of the genetic code file.

   This is followed by the description of the code and then by four lines
   giving the IUPAC one-letter code of the translated amino acid, the
   start codons (indicdated by an 'M') and the three bases of the codon,
   lined up one on top of the other.

   For example:

------------------------------------------------------------------------------
# Genetic Code Table
#
# Obtained from: http://www.ncbi.nlm.nih.gov/collab/FT/genetic_codes.html
# and: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
#
# Differs from Genetic Code [1] only in that the initiation sites have been
# changed to only 'AUG'

Genetic Code [0]
Standard

AAs  =   FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
------------------------------------------------------------------------------

Notes

   If you have selected one of the options to report a regions around a
   START or STOP codon, then note that any such region that crosses the
   beginning or end of the sequence will not be reported.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   '-sbegin' and -send' do not work with this program.

See also

   Program name                        Description
   marscan      Finds MAR/SAR sites in nucleic sequences
   plotorf      Plot potential open reading frames
   showorf      Pretty output of DNA translations
   sixpack      Display a DNA sequence with 6-frame translation and ORFs
   syco         Synonymous codon usage Gribskov statistic plot
   tcode        Fickett TESTCODE statistic to identify protein-coding DNA
   wobble       Wobble base plot

     * checktrans - Reports STOP codons and ORF statistics of a protein
       sequence

Author(s)

   Gary Williams (gwilliam