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checktrans |
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.
% checktrans Reports STOP codons and ORF statistics of a protein Input sequence(s): ../../data/paamir.pep Minimum ORF Length to report [100]: Output file [paamir_1.checktrans]: Output sequence [paamir_1.fasta]: |
Go to the input files for this example
Go to the output files for this example
Mandatory qualifiers: [-sequence] seqall Sequence database USA -orfml integer Minimum ORF Length to report [-report] outfile Output file name -outseq seqoutall Sequence file to hold output ORF sequences Optional qualifiers: -[no]addlast boolean 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 qualifiers: -featout featout File for output features Associated qualifiers: "-sequence" related qualifiers -sbegin1 integer First base used -send1 integer Last base used, def=seq length -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 -sopenfile1 string Input filename -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-report" related qualifiers -odirectory2 string Output directory "-outseq" related qualifiers -osformat string Output seq format -osextension string File name extension -osname string Base file name -osdirectory string Output directory -osdbname string Database name to add -ossingle boolean Separate file for each entry -oufo string UFO features -offormat string Features format -ofname string Features file name -ofdirectory string Output directory "-featout" related qualifiers -offormat string Output feature format -ofopenfile string Features file name -ofextension string File name extension -ofdirectory string Output directory -ofname string Base file name -ofsingle 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 required and optional values -debug boolean Write debug output to program.dbg -acdlog boolean Write ACD processing log to program.acdlog -acdpretty boolean Rewrite ACD file as program.acdpretty -acdtable boolean Write HTML table of options -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 deaths |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-orfml | Minimum ORF Length to report | Integer 1 or more | 100 |
[-report] (Parameter 2) |
Output file name | Output file | <sequence>.checktrans |
-outseq | Sequence file to hold output ORF sequences | Writeable sequence(s) | <sequence>.format |
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 qualifiers | Allowed values | Default | |
-featout | File for output features | Writeable feature table | unknown.gff |
>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 |
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 2003-05-22 ##Type Protein PAAMIR_1 PAAMIR_1 checktrans misc_feature 278 634 0.000 + . Sequence "PAAMIR_1.1" |
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').
Program name | Description |
---|---|
backtranseq | Back translate a protein sequence |
charge | Protein charge plot |
compseq | Counts the 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 |
Gary Williams (gwilliam © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK
to output
the sequence data to a single file in the conventional EMBOSS style.
Rewritten 2 March 2000 - Gary Williams