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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.
% transeq embl:paamir paamir.pep -auto % checktrans Input sequence: paamir.pep Minimum ORF Length to report [100]: 30 Output file [paamir_1.checktrans]: Output sequence [paamir_1.fasta]:
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: (none) Advanced qualifiers: -featout featout File for output features General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
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 | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-featout | File for output features | Writeable feature table | unknown.gff |
The ORF report file from the above example run is:
CHECKTRANS of PAAMIR_1 from 1 to 723 ORF# Pos Len ORF Range Sequence name 1 54 53 1-53 PAAMIR_1_1 3 136 52 84-135 PAAMIR_1_3 4 180 43 137-179 PAAMIR_1_4 6 277 72 205-276 PAAMIR_1_6 7 635 357 278-634 PAAMIR_1_7 Total STOPS: 7
This 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.
The output sequence file is:
>PAAMIR_1_1 GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR >PAAMIR_1_3 TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGGYGSSWAATCRTRARR >PAAMIR_1_4 CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT >PAAMIR_1_6 CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTRRAPTWSSPPWWAPAPPSCIAPSPV ATATAGGRRSPA >PAAMIR_1_7 PPARRRWRRWRVTWQRGRWWSRLTSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGR PCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR SAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRP GLAADPHRLFGAPVLAAAGSLRRAGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGV RKPRGALADHRAGVPRRDHPAARCPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGP DQPGQGVADAAPWLGRARGAPAPVAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ
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 |
It was rewritten by Gary Williams(gwilliam@hgmp.mrc.ac.uk) to output the sequence data to a single file in the conventional EMBOSS style.
Rewritten 2 March 2000 - Gary Williams