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.
% checktrans Reports STOP codons and ORF statistics of a protein Input protein sequence(s): paamir.pep Minimum ORF Length to report : Output file [paamir_1.checktrans]: output sequence(s) [paamir_1.fasta]: Features output [paamir_1.gff]:
Go to the input files for this example
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Standard (Mandatory) qualifiers: [-sequence] seqall Protein sequence(s) filename and optional format, or reference (input USA) -orfml integer  Minimum ORF Length to report (Integer 1 or more) [-outfile] outfile [*.checktrans] Output file name [-outseq] seqoutall [
|Standard (Mandatory) qualifiers||Allowed values||Default|
|Protein sequence(s) filename and optional format, or reference (input USA)||Readable sequence(s)||Required|
|-orfml||Minimum ORF Length to report||Integer 1 or more||100|
|Output file name||Output file||<*>.checktrans|
|Sequence file to hold output ORF sequences||Writeable sequence(s)||<*>.format|
|File for output features||Writeable feature table||unknown.gff|
|Additional (Optional) qualifiers||Allowed values||Default|
|-[no]addlast||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.||Boolean value Yes/No||Yes|
|Advanced (Unprompted) qualifiers||Allowed values||Default|
>PAAMIR_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR*SACCSP KPASPPISSARTRMAHCSRSSN*TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGG YGSSWAATCRTRARR*CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT* FATTASGWCSSARTTSIRGKATM*CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTR RAPTWSSPPWWAPAPPSCIAPSPVATATAGGRRSPA*PPARRRWRRWRVTWQRGRWWSRL TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG PPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRPGLAADPHRLFGAPVLAAAGSLRR AGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGVRKPRGALADHRAGVPRRDHPAAR CPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGPDQPGQGVADAAPWLGRARGAPAP VAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ*QEGYRHHAGTGSAVRWRGAVSQCRL VAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSRAGLAEGRSADPAIRFYLSVGGRQPV PRX
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').
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
>PAAMIR_1_7 PPARRRWRRWRVTWQRGRWWSRLTSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGR PCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR SAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRP GLAADPHRLFGAPVLAAAGSLRRAGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGV RKPRGALADHRAGVPRRDHPAARCPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGP DQPGQGVADAAPWLGRARGAPAPVAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ
##gff-version 2.0 ##date 2007-07-15 ##Type Protein PAAMIR_1 PAAMIR_1 checktrans region 278 634 0.000 + . Sequence "PAAMIR_1.1"
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.
|backtranambig||Back-translate a protein sequence to ambiguous nucleotide sequence|
|backtranseq||Back-translate a protein sequence to a nucleotide sequence|
|charge||Draw a protein charge plot|
|compseq||Calculate the composition of unique words in sequences|
|emowse||Search protein sequences by digest fragment molecular weight|
|freak||Generate residue/base frequency table or plot|
|iep||Calculate the isoelectric point of proteins|
|mwcontam||Find weights common to multiple molecular weights files|
|mwfilter||Filter noisy data from molecular weights file|
|octanol||Draw a White-Wimley protein hydropathy plot|
|pepinfo||Plot amino acid properties of a protein sequence in parallel|
|pepstats||Calculates statistics of protein properties|
|pepwindow||Draw a Kyte-Doolittle hydropathy plot for a protein sequence|
|pepwindowall||Draw Kyte-Doolittle hydropathy plot for a protein alignment|
|wordcount||Count and extract unique words in DNA sequence(s)|
Modified 2 March 2000 - Gary Williams