| ## EMBOSS: checktrans

# Program checktrans

## Function

Reports STOP codons and ORF statistics of a protein sequence

## Description

Reads in a protein sequence containing stops, and writes a report of any open reading frames (continuous protein sequence with no stops) that are greater than a minimum size. The default minimum ORF size is 100 residues. It writes out any ORF sequences.

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.

## Usage

Here is a sample session with checktrans, using the output from a transeq run.

    % 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]:

## Command line arguments

       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                bool       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

## Input file format

This program reads the USA of a protein sequence with STOP codons in it.

## Output file format

This program writes two files: the ORF report file and the output sequence file.

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

## Data files

None.

## Notes

None.

## 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
--- | ---
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
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

- transeq : Translate nucleic acid sequences
- getorf : Finds and extracts open reading frames (ORFs)
- plotorf : Plot potential open reading frames
- showseq : Display a sequence with features, translation etc..

## Author(s)

This application was written by Rodrigo Lopez (rls@ebi.ac.uk) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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.

## History

Completed 24 Feb 2000 - Rodrigo Lopez

Rewritten 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