EMBOSS: getorf manual

getorf

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Function

Find and extract open reading frames (ORFs)

Description

This program finds and outputs the sequences of open reading frames (ORFs) in one or more nucleotide sequences. An ORF may be defined as a region of a specified minimum size between two STOP codons, or between a START and a STOP codon. The ORFs can be output as the nucleotide sequence or as the protein translation. Optionally, the program will output the region around the START codon, the first STOP codon, or the final STOP codon of an ORF. The START and STOP codons are defined in a Genetic Code table; a suitable table can be selected for the organism you are investigating. 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).

Usage

Here is a sample session with getorf


% getorf -minsize 300 
Find and extract open reading frames (ORFs)
Input nucleotide sequence(s): tembl:v00294
protein output sequence(s) [v00294.orf]:

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

Command line arguments

Find and extract open reading frames (ORFs)
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outseq]            seqoutall  [.] Protein sequence
                                  set(s) filename and optional format (output
                                  USA)

   Additional (Optional) qualifiers:
   -table              menu       [0] Code to use (Values: 0 (Standard); 1
                                  (Standard (with alternative initiation
                                  codons)); 2 (Vertebrate Mitochondrial); 3
                                  (Yeast Mitochondrial); 4 (Mold, Protozoan,
                                  Coelenterate Mitochondrial and
                                  Mycoplasma/Spiroplasma); 5 (Invertebrate
                                  Mitochondrial); 6 (Ciliate Macronuclear and
                                  Dasycladacean); 9 (Echinoderm
                                  Mitochondrial); 10 (Euplotid Nuclear); 11
                                  (Bacterial); 12 (Alternative Yeast Nuclear);
                                  13 (Ascidian Mitochondrial); 14 (Flatworm
                                  Mitochondrial); 15 (Blepharisma
                                  Macronuclear); 16 (Chlorophycean
                                  Mitochondrial); 21 (Trematode
                                  Mitochondrial); 22 (Scenedesmus obliquus);
                                  23 (Thraustochytrium Mitochondrial))
   -minsize            integer    [30] Minimum nucleotide size of ORF to
                                  report (Any integer value)
   -maxsize            integer    [1000000] Maximum nucleotide size of ORF to
                                  report (Any integer value)
   -find               menu       [0] This is a small menu of possible output
                                  options. The first four options are to
                                  select either the protein translation or the
                                  original nucleic acid sequence of the open
                                  reading frame. There are two possible
                                  definitions of an open reading frame: it can
                                  either be a region that is free of STOP
                                  codons or a region that begins with a START
                                  codon and ends with a STOP codon. The last
                                  three options are probably only of interest
                                  to people who wish to investigate the
                                  statistical properties of the regions around
                                  potential START or STOP codons. The last
                                  option assumes that ORF lengths are
                                  calculated between two STOP codons. (Values:
                                  0 (Translation of regions between STOP
                                  codons); 1 (Translation of regions between
                                  START and STOP codons); 2 (Nucleic sequences
                                  between STOP codons); 3 (Nucleic sequences
                                  between START and STOP codons); 4
                                  (Nucleotides flanking START codons); 5
                                  (Nucleotides flanking initial STOP codons);
                                  6 (Nucleotides flanking ending STOP codons))

   Advanced (Unprompted) qualifiers:
   -[no]methionine     boolean    [Y] START codons at the beginning of protein
                                  products will usually code for Methionine,
                                  despite what the codon will code for when it
                                  is internal to a protein. This qualifier
                                  sets all such START codons to code for
                                  Methionine by default.
   -circular           boolean    [N] Is the sequence circular
   -[no]reverse        boolean    [Y] Set this to be false if you do not wish
                                  to find ORFs in the reverse complement of
                                  the sequence.
   -flanking           integer    [100] If you have chosen one of the options
                                  of the type of sequence to find that gives
                                  the flanking sequence around a STOP or START
                                  codon, this allows you to set the number of
                                  nucleotides either side of that codon to
                                  output. If the region of flanking
                                  nucleotides crosses the start or end of the
                                  sequence, no output is given for this codon.
                                  (Any integer value)

   Associated qualifiers:

   "-sequence" 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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 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

Qualifier

Type

Description

Allowed values

Default

Standard (Mandatory) qualifiers

[-sequence]
(Parameter 1)

seqall

Nucleotide sequence(s) filename and optional format, or reference (input USA)

Readable sequence(s)

Required

[-outseq]
(Parameter 2)

seqoutall

Protein sequence set(s) filename and optional format (output USA)

Writeable sequence(s)

<*>.format

Additional (Optional) qualifiers

-table

list

Code to use

0	(Standard)
1	(Standard (with alternative initiation codons))
2	(Vertebrate Mitochondrial)
3	(Yeast Mitochondrial)
4	(Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma)
5	(Invertebrate Mitochondrial)
6	(Ciliate Macronuclear and Dasycladacean)
9	(Echinoderm Mitochondrial)
10	(Euplotid Nuclear)
11	(Bacterial)
12	(Alternative Yeast Nuclear)
13	(Ascidian Mitochondrial)
14	(Flatworm Mitochondrial)
15	(Blepharisma Macronuclear)
16	(Chlorophycean Mitochondrial)
21	(Trematode Mitochondrial)
22	(Scenedesmus obliquus)
23	(Thraustochytrium Mitochondrial)

-minsize

integer

Minimum nucleotide size of ORF to report

Any integer value

-maxsize

integer

Maximum nucleotide size of ORF to report

Any integer value

1000000

-find

list

This is a small menu of possible output options. The first four options are to select either the protein translation or the original nucleic acid sequence of the open reading frame. There are two possible definitions of an open reading frame: it can either be a region that is free of STOP codons or a region that begins with a START codon and ends with a STOP codon. The last three options are probably only of interest to people who wish to investigate the statistical properties of the regions around potential START or STOP codons. The last option assumes that ORF lengths are calculated between two STOP codons.

0	(Translation of regions between STOP codons)
1	(Translation of regions between START and STOP codons)
2	(Nucleic sequences between STOP codons)
3	(Nucleic sequences between START and STOP codons)
4	(Nucleotides flanking START codons)
5	(Nucleotides flanking initial STOP codons)
6	(Nucleotides flanking ending STOP codons)

Advanced (Unprompted) qualifiers

-[no]methionine

boolean

START codons at the beginning of protein products will usually code for Methionine, despite what the codon will code for when it is internal to a protein. This qualifier sets all such START codons to code for Methionine by default.

Boolean value Yes/No

Yes

-circular

boolean

Is the sequence circular

Boolean value Yes/No

-[no]reverse

boolean

Set this to be false if you do not wish to find ORFs in the reverse complement of the sequence.

Boolean value Yes/No

Yes

-flanking

integer

If you have chosen one of the options of the type of sequence to find that gives the flanking sequence around a STOP or START codon, this allows you to set the number of nucleotides either side of that codon to output. If the region of flanking nucleotides crosses the start or end of the sequence, no output is given for this codon.

Any integer value

100

Associated qualifiers

"-sequence" associated seqall qualifiers

-sbegin1
-sbegin_sequence

integer

Start of each sequence to be used

Any integer value

-send1
-send_sequence

integer

End of each sequence to be used

Any integer value

-sreverse1
-sreverse_sequence

boolean

Reverse (if DNA)

Boolean value Yes/No

-sask1
-sask_sequence

boolean

Ask for begin/end/reverse

Boolean value Yes/No

-snucleotide1
-snucleotide_sequence

boolean

Sequence is nucleotide

Boolean value Yes/No

-sprotein1
-sprotein_sequence

boolean

Sequence is protein

Boolean value Yes/No

-slower1
-slower_sequence

boolean

Make lower case

Boolean value Yes/No

-supper1
-supper_sequence

boolean

Make upper case

Boolean value Yes/No

-scircular1
-scircular_sequence

boolean

Sequence is circular

Boolean value Yes/No

-squick1
-squick_sequence

boolean

Read id and sequence only

Boolean value Yes/No

-sformat1
-sformat_sequence

string

Input sequence format

Any string

-iquery1
-iquery_sequence

string

Input query fields or ID list

Any string

-ioffset1
-ioffset_sequence

integer

Input start position offset

Any integer value

-sdbname1
-sdbname_sequence

string

Database name

Any string

-sid1
-sid_sequence

string

Entryname

Any string

-ufo1
-ufo_sequence

string

UFO features

Any string

-fformat1
-fformat_sequence

string

Features format

Any string

-fopenfile1
-fopenfile_sequence

string

Features file name

Any string

"-outseq" associated seqoutall qualifiers

-osformat2
-osformat_outseq

string

Output seq format

Any string

-osextension2
-osextension_outseq

string

File name extension

Any string

-osname2
-osname_outseq

string

Base file name

Any string

-osdirectory2
-osdirectory_outseq

string

Output directory

Any string

-osdbname2
-osdbname_outseq

string

Database name to add

Any string

-ossingle2
-ossingle_outseq

boolean

Separate file for each entry

Boolean value Yes/No

-oufo2
-oufo_outseq

string

UFO features

Any string

-offormat2
-offormat_outseq

string

Features format

Any string

-ofname2
-ofname_outseq

string

Features file name

Any string

-ofdirectory2
-ofdirectory_outseq

string

Output directory

Any string

General qualifiers

-auto

boolean

Turn off prompts

Boolean value Yes/No

-stdout

boolean

Write first file to standard output

Boolean value Yes/No

-filter

boolean

Read first file from standard input, write first file to standard output

Boolean value Yes/No

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

-help

boolean

Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose

Boolean value Yes/No

-warning

boolean

Report warnings

Boolean value Yes/No

-error

boolean

Report errors

Boolean value Yes/No

-fatal

boolean

Report fatal errors

Boolean value Yes/No

-die

boolean

Report dying program messages

Boolean value Yes/No

-version

boolean

Report version number and exit

Boolean value Yes/No

Input file format

getorf reads one or more nucleotide sequences.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

Input files for usage example

'tembl:v00294' is a sequence entry in the example nucleic acid database 'tembl'

Database entry: tembl:v00294

ID   V00294; SV 1; linear; genomic DNA; STD; PRO; 1113 BP.
XX
AC   V00294;
XX
DT   09-JUN-1982 (Rel. 01, Created)
DT   10-FEB-1999 (Rel. 58, Last updated, Version 2)
XX
DE   E. coli laci gene (codes for the lac repressor).
XX
KW   DNA binding protein; repressor.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC   Enterobacteriaceae; Escherichia.
XX
RN   [1]
RP   1-1113
RX   DOI; 10.1038/274765a0.
RX   PUBMED; 355891.
RA   Farabaugh P.J.;
RT   "Sequence of the lacI gene";
RL   Nature 274(5673):765-769(1978).
XX
CC   KST ECO.LACI
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1113
FT                   /organism="Escherichia coli"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:562"
FT   CDS             31..1113
FT                   /transl_table=11
FT                   /note="reading frame"
FT                   /db_xref="GOA:P03023"
FT                   /db_xref="InterPro:IPR000843"
FT                   /db_xref="InterPro:IPR010982"
FT                   /db_xref="PDB:1CJG"
FT                   /db_xref="PDB:1EFA"
FT                   /db_xref="PDB:1JWL"
FT                   /db_xref="PDB:1JYE"
FT                   /db_xref="PDB:1JYF"
FT                   /db_xref="PDB:1L1M"
FT                   /db_xref="PDB:1LBG"
FT                   /db_xref="PDB:1LBH"
FT                   /db_xref="PDB:1LBI"
FT                   /db_xref="PDB:1LCC"
FT                   /db_xref="PDB:1LCD"
FT                   /db_xref="PDB:1LQC"
FT                   /db_xref="PDB:1LTP"
FT                   /db_xref="PDB:1OSL"
FT                   /db_xref="PDB:1TLF"
FT                   /db_xref="PDB:1Z04"
FT                   /db_xref="PDB:2BJC"
FT                   /db_xref="PDB:2KEI"
FT                   /db_xref="PDB:2KEJ"
FT                   /db_xref="PDB:2KEK"
FT                   /db_xref="PDB:2P9H"
FT                   /db_xref="PDB:2PAF"
FT                   /db_xref="PDB:2PE5"
FT                   /db_xref="PDB:3EDC"
FT                   /db_xref="UniProtKB/Swiss-Prot:P03023"
FT                   /protein_id="CAA23569.1"
FT                   /translation="MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAEL
FT                   NYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGV
FT                   EACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSH
FT                   EDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSA
FT                   MSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSC
FT                   YIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPR
FT                   ALADSLMQLARQVSRLESGQ"
XX
SQ   Sequence 1113 BP; 249 A; 304 C; 322 G; 238 T; 0 other;
     ccggaagaga gtcaattcag ggtggtgaat gtgaaaccag taacgttata cgatgtcgca        60
     gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg tgaaccaggc cagccacgtt       120
     tctgcgaaaa cgcgggaaaa agtggaagcg gcgatggcgg agctgaatta cattcccaac       180
     cgcgtggcac aacaactggc gggcaaacag tcgttgctga ttggcgttgc cacctccagt       240
     ctggccctgc acgcgccgtc gcaaattgtc gcggcgatta aatctcgcgc cgatcaactg       300
     ggtgccagcg tggtggtgtc gatggtagaa cgaagcggcg tcgaagcctg taaagcggcg       360
     gtgcacaatc ttctcgcgca acgcgtcagt gggctgatca ttaactatcc gctggatgac       420
     caggatgcca ttgctgtgga agctgcctgc actaatgttc cggcgttatt tcttgatgtc       480
     tctgaccaga cacccatcaa cagtattatt ttctcccatg aagacggtac gcgactgggc       540
     gtggagcatc tggtcgcatt gggtcaccag caaatcgcgc tgttagcggg cccattaagt       600
     tctgtctcgg cgcgtctgcg tctggctggc tggcataaat atctcactcg caatcaaatt       660
     cagccgatag cggaacggga aggcgactgg agtgccatgt ccggttttca acaaaccatg       720
     caaatgctga atgagggcat cgttcccact gcgatgctgg ttgccaacga tcagatggcg       780
     ctgggcgcaa tgcgcgccat taccgagtcc gggctgcgcg ttggtgcgga tatctcggta       840
     gtgggatacg acgataccga agacagctca tgttatatcc cgccgtcaac caccatcaaa       900
     caggattttc gcctgctggg gcaaaccagc gtggaccgct tgctgcaact ctctcagggc       960
     caggcggtga agggcaatca gctgttgccc gtctcactgg tgaaaagaaa aaccaccctg      1020
     gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat gcagctggca      1080
     cgacaggttt cccgactgga aagcgggcag tga                                   1113
//

Output file format

The input is a standard EMBOSS sequence query (also known as a 'USA') with associated feature information.

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: text, html, xml (uniprotxml), obo, embl (swissprot)

Where the sequence format has no feature information, a second file can be read to load the feature data. The file is specified with the qualifier -ufo xxx and the feature format is specified with the qualifier -fformat xxx

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

See: http://emboss.sf.net/docs/themes/FeatureFormats.html for further information on feature formats.

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: v00294.orf

>V00294_1 [735 - 1112] E. coli laci gene (codes for the lac repressor).
GHRSHCDAGCQRSDGAGRNARHYRVRAARWCGYLGSGIRRYRRQLMLYPAVNHHQTGFSP
AGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFP
TGKRAV
>V00294_2 [1 - 1110] E. coli laci gene (codes for the lac repressor).
PEESQFRVVNVKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPN
RVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAA
VHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLG
VEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTM
QMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIK
QDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLA
RQVSRLESGQ
>V00294_3 [465 - 49] (REVERSE SENSE) E. coli laci gene (codes for the lac repressor).
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, >V00294_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

There are two common definitions of an open reading frame: it can either be a region that is free of STOP codons or a region that begins with a START codon and ends with a STOP codon.

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.

Program name	Description
checktrans	Report STOP codons and ORF statistics of a protein
marscan	Find matrix/scaffold recognition (MRS) signatures in DNA sequences
plotorf	Plot potential open reading frames in a nucleotide sequence
showorf	Display a nucleotide sequence and translation in pretty format
sixpack	Display a DNA sequence with 6-frame translation and ORFs
syco	Draw synonymous codon usage statistic plot for a nucleotide sequence
tcode	Identify protein-coding regions using Fickett TESTCODE statistic
wobble	Plot third base position variability in a nucleotide sequence

Author(s)

Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

2000 - written - Gary Williams

November 2002 - added indication of reverse sense ORFs

November 2002 - added indication of ORFs that cross the breakpoint at position 1 in circular genomes.

Target users

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

Comments

None

Wiki

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: tembl:v00294

Output file format

Output files for usage example

File: v00294.orf

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments