| checktrans

## Function

Reports STOP codons and ORF statistics of a protein

## 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

    % checktrans
    Reports STOP codons and ORF statistics of a protein
    Input sequence(s): ../../data/paamir.pep
    Minimum ORF Length to report [100]:
    Output file [paamir_1.checktrans]:
    Output sequence [paamir_1.fasta]:

Go to the input files for this example
Go to the output files for this example

## 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:
       -[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.

       Advanced qualifiers:
       -featout            featout    File for output features

       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-report" related qualifiers
       -odirectory2         string     Output directory
      "-outseq" related qualifiers
       -osformat            string     Output seq format
       -osextension         string     File name extension
       -osname              string     Base file name
       -osdirectory         string     Output directory
       -osdbname            string     Database name to add
       -ossingle            boolean    Separate file for each entry
       -oufo                string     UFO features
       -offormat            string     Features format
       -ofname              string     Features file name
       -ofdirectory         string     Output directory
      "-featout" related qualifiers
       -offormat            string     Output feature format
       -ofopenfile          string     Features file name
       -ofextension         string     File name extension
       -ofdirectory         string     Output directory
       -ofname              string     Base file name
       -ofsingle            boolean    Separate file for each entry

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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 deaths

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
-[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 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.

### Input files for usage example

### File: ../../data/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 (paamir_1.checktrans), the output sequence file (paamir_1.fasta) and the feature file (paamir_1.out3) which is in GFF format by default.

### 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 2003-05-22
    ##Type Protein PAAMIR_1
    PAAMIR_1	checktrans	misc_feature	278	634	0.000	+	.	Sequence "PAAMIR_1.1"

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. 'PAAMIR_1_7').

## 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
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

- 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

Gary Williams (gwilliam © hgmp.mrc.ac.uk)
HGMP-RC, 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

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