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checktrans
Function
Reports STOP codons and ORF statistics of a protein
Description
Reads in a protein sequence containing stops, and writes a report of
any open reading frames (continuous protein sequence with no stops)
that are greater than a minimum size. The default minimum ORF size is
100 residues. It writes out any ORF sequences.
The input sequence might typically have been produced by transeq.
Note that if you have only translated a nucleic sequence in one frame,
checktrans will miss possible ORFs in other frames. You have to give
checktrans translations in all three (six?) frames in order for it to
be effective at finding all possible ORFs.
Usage
Here is a sample session with checktrans
% checktrans
Reports 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
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
-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
"-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 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 dying program messages
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 regul
ation
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
(paamir_1.checktrans), the output sequence file (paamir_1.fasta) and
the feature file (paamir_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. 'PAAMIR_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 2.0
##date 2006-07-15
##Type Protein PAAMIR_1
PAAMIR_1 checktrans misc_feature 278 634 0.000 +
. Sequence "PAAMIR_1.1"
Data files
None.
Notes
None.
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 codons
backtranseq Back translate a protein sequence
charge Protein charge plot
compseq Count composition of dimer/trimer/etc words in a sequence
emowse Protein identification by mass spectrometry
freak Residue/base frequency table or plot
iep Calculates the isoelectric point of a protein
mwcontam Shows molwts that match across a set of files
mwfilter Filter noisy molwts from mass spec output
octanol Displays protein hydropathy
pepinfo Plots simple amino acid properties in parallel
pepstats Protein statistics
pepwindow Displays protein hydropathy
pepwindowall Displays protein hydropathy of a set of sequences
Author(s)
Rodrigo Lopez (rls ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK and modified by Gary Williams
(gwilliam rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
Genome Campus, Hinxton, Cambridge, CB10 1SB, UK to output the sequence
data to a single file in the conventional EMBOSS style.
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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