Appdoc:Checktrans
From EMBOSS
Contents |
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
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) | seqall | Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| -orfml | integer | Minimum ORF Length to report | Integer 1 or more | 100 |
| [-outfile] (Parameter 2) | outfile | Output file name | Output file | <*>.checktrans |
| [-outseq] (Parameter 3) | seqoutall | Sequence file to hold output ORF sequences | Writeable sequence(s) | <*>.format |
| [-outfeat] (Parameter 4) | featout | File for output features | Writeable feature table | unknown.gff |
| Additional (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. | Boolean value Yes/No | Yes |
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated seqall qualifiers | ||||
| -sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence | string | Input sequence format | Any string | |
| -sdbname1 -sdbname_sequence | string | Database name | Any string | |
| -sid1 -sid_sequence | string | Entryname | Any string | |
| -ufo1 -ufo_sequence | string | UFO features | Any string | |
| -fformat1 -fformat_sequence | string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence | string | Features file name | Any string | |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory2 -odirectory_outfile | string | Output directory | Any string | |
| "-outseq" associated seqoutall qualifiers | ||||
| -osformat3 -osformat_outseq | string | Output seq format | Any string | |
| -osextension3 -osextension_outseq | string | File name extension | Any string | |
| -osname3 -osname_outseq | string | Base file name | Any string | |
| -osdirectory3 -osdirectory_outseq | string | Output directory | Any string | |
| -osdbname3 -osdbname_outseq | string | Database name to add | Any string | |
| -ossingle3 -ossingle_outseq | boolean | Separate file for each entry | Boolean value Yes/No | N |
| -oufo3 -oufo_outseq | string | UFO features | Any string | |
| -offormat3 -offormat_outseq | string | Features format | Any string | |
| -ofname3 -ofname_outseq | string | Features file name | Any string | |
| -ofdirectory3 -ofdirectory_outseq | string | Output directory | Any string | |
| "-outfeat" associated featout qualifiers | ||||
| -offormat4 -offormat_outfeat | string | Output feature format | Any string | |
| -ofopenfile4 -ofopenfile_outfeat | string | Features file name | Any string | |
| -ofextension4 -ofextension_outfeat | string | File name extension | Any string | |
| -ofdirectory4 -ofdirectory_outfeat | string | Output directory | Any string | |
| -ofname4 -ofname_outfeat | string | Base file name | Any string | |
| -ofsingle4 -ofsingle_outfeat | boolean | Separate file for each entry | Boolean value Yes/No | N |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
Input file format
This program reads the USA of a protein sequence with STOP codons in it.
Input example
File: paamir.pep
>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
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 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 2009-07-15 #!Type Protein #!Source-version EMBOSS 6.1.0 PAAMIR_1 checktrans polypeptide_region 278 634 0.000 + . 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
| 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 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) |
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 (@) emboss.open-bio.org) not to the original author.
and modified 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 (@) emboss.open-bio.org) not to the original author.
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
