EMBOSS: checktrans

| checktrans

## 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

       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. 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

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | 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
[-outfile] (Parameter 2) | Output file name | Output file | <*>.checktrans
[-outseq] (Parameter 3) | Sequence file to hold output ORF sequences | Writeable sequence(s) | <*>.format
[-outfeat] (Parameter 4) | 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
(none)

## 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 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 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 2.0
    ##date 2007-07-15
    ##Type Protein PAAMIR_1
    PAAMIR_1	checktrans	region	278	634	0.000	+	.	Sequence "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
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)

## Author(s)

Rodrigo Lopez (rls © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and modified by Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK 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