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 Reports 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 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 Reports STOP codons and ORF statistics of a protein Version: EMBOSS:6.4.0.0 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 -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 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 2011-07-15 #!Type Protein #!Source-version EMBOSS 6.4.0.0 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 Finds and extracts open reading frames (ORFs) marscan Finds 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 Displays 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