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checktrans
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Report STOP codons and ORF statistics of a protein
Description
checktrans reads a protein sequence containing stop characters and
writes a statistical report of any open reading frames (ORFs) that are
greater than a minimum size. An open reading frame is defined as a
continuous region of protein sequence with no stop characters. The
default minimum ORF size is 100 residues. In addition to the report
output, any ORF sequences are written to file and features of those
sequences written to a separate file.
Usage
Here is a sample session with checktrans
% checktrans
Report STOP codons and ORF statistics of a protein
Input protein sequence(s): paamir.pep
Minimum ORF Length to report [100]:
Output file [paamir_1.checktrans]:
output sequence(s) [paamir_1.fasta]:
Features output [paamir_1.gff]:
Go to the input files for this example
Go to the output files for this example
Command line arguments
Report STOP codons and ORF statistics of a protein
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqall Protein sequence(s) filename and optional
format, or reference (input USA)
-orfml integer [100] Minimum ORF Length to report (Integer
1 or more)
[-outfile] outfile [*.checktrans] Output file name
[-outseq] seqoutall [.] Sequence file to hold
output ORF sequences
[-outfeat] featout [unknown.gff] File for output features
Additional (Optional) qualifiers:
-[no]addlast boolean [Y] An asterisk in the protein sequence
indicates the position of a STOP codon.
Checktrans assumes that all ORFs end in a
STOP codon. Forcing the sequence to end with
an asterisk, if there is not one there
already, makes checktrans treat the end as a
potential ORF. If an asterisk is added, it
is not included in the reported count of
STOPs.
Advanced (Unprompted) qualifiers: (none)
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
"-outfile" associated qualifiers
-odirectory2 string Output directory
"-outseq" associated qualifiers
-osformat3 string Output seq format
-osextension3 string File name extension
-osname3 string Base file name
-osdirectory3 string Output directory
-osdbname3 string Database name to add
-ossingle3 boolean Separate file for each entry
-oufo3 string UFO features
-offormat3 string Features format
-ofname3 string Features file name
-ofdirectory3 string Output directory
"-outfeat" associated qualifiers
-offormat4 string Output feature format
-ofopenfile4 string Features file name
-ofextension4 string File name extension
-ofdirectory4 string Output directory
-ofname4 string Base file name
-ofsingle4 boolean Separate file for each entry
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
Input file format
This program reads the USA of a protein sequence with STOP codons in
it.
Input files for usage example
File: paamir.pep
>PAAMIR_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regula
tion
GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR*SACCSP
KPASPPISSARTRMAHCSRSSN*TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGG
YGSSWAATCRTRARR*CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT*
FATTASGWCSSARTTSIRGKATM*CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTR
RAPTWSSPPWWAPAPPSCIAPSPVATATAGGRRSPA*PPARRRWRRWRVTWQRGRWWSRL
TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC
TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG
PPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRPGLAADPHRLFGAPVLAAAGSLRR
AGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGVRKPRGALADHRAGVPRRDHPAAR
CPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGPDQPGQGVADAAPWLGRARGAPAP
VAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ*QEGYRHHAGTGSAVRWRGAVSQCRL
VAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSRAGLAEGRSADPAIRFYLSVGGRQPV
PRX
Output file format
This program writes three files: the ORF report file
(x13776_1.checktrans), the output sequence file (x13776_1.fasta) and
the feature file (x13776_1.out3) which is in GFF format by default.
The ORF report file gives the numeric count of the ORF, the position of
the terminating STOP codon, the length of the ORF, its start and end
positions and the name of the sequence it has been written out as.
The name of the output sequences is constructed from the name of the
input sequence followed by an underscore and then the numeric count of
the ORF (e.g. 'X13776_1_7').
Output files for usage example
File: paamir_1.checktrans
CHECKTRANS of PAAMIR_1 from 1 to 724
ORF# Pos Len ORF Range Sequence name
7 635 357 278-634 PAAMIR_1_7
Total STOPS: 7
File: paamir_1.fasta
>PAAMIR_1_7
PPARRRWRRWRVTWQRGRWWSRLTSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGR
PCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR
SAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRP
GLAADPHRLFGAPVLAAAGSLRRAGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGV
RKPRGALADHRAGVPRRDHPAARCPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGP
DQPGQGVADAAPWLGRARGAPAPVAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ
File: paamir_1.gff
##gff-version 3
##sequence-region PAAMIR_1 1 634
#!Date 2013-07-15
#!Type Protein
#!Source-version EMBOSS 6.6.0.0
PAAMIR_1 checktrans polypeptide_region 278 634 .
. . ID=PAAMIR_1.1
Data files
None.
Notes
A reading frame is a relative position in DNA or RNA from which
contiguous, non-overlapping codons are read during transcription. There
are 3 possible reading frames in mRNA strand and six in a double
stranded DNA where transcription is possible from either strand. An
open reading frame (ORF) is a reading frame that begins with a start
codon and includes the subsequent transcribed region, stopping
immediately before the first stop codon.
Where you have a nucleotide sequence for analysis, it should first be
translated by using transeq. The transeq output file will then serve as
the input to checktrans. Note that if you have only translated a
nucleic sequence in one frame, checktrans will miss possible ORFs in
the other frames. You must provide checktrans with translations in all
three (six?) frames in order for it to be effective at finding all
possible ORFs.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
This program always exits with a status of 0.
Known bugs
None.
See also
Program name Description
backtranambig Back-translate a protein sequence to ambiguous nucleotide
sequence
backtranseq Back-translate a protein sequence to a nucleotide sequence
coderet Extract CDS, mRNA and translations from feature tables
getorf Find and extract open reading frames (ORFs)
marscan Find matrix/scaffold recognition (MRS) signatures in DNA
sequences
plotorf Plot potential open reading frames in a nucleotide sequence
prettyseq Write a nucleotide sequence and its translation to file
remap Display restriction enzyme binding sites in a nucleotide sequence
showorf Display a nucleotide sequence and translation in pretty format
showseq Display sequences with features 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
transeq Translate nucleic acid sequences
wobble Plot third base position variability in a nucleotide sequence
Author(s)
Rodrigo Lopez
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author. and
modified to output the sequence data to a single file in the
conventional EMBOSS style by Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
History
Completed 24 Feb 2000 - Rodrigo Lopez
Modified 2 March 2000 - Gary Williams
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
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