
                                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): paamir.pep
Minimum ORF Length to report [100]: 
Output file [paamir_1.checktrans]: 
Output sequence [paamir_1.fasta]: 
Output features [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     Sequence database USA
   -orfml              integer    Minimum ORF Length to report
  [-outfile]           outfile    Output file name
  [-outseq]            seqoutall  Sequence file to hold output ORF sequences
  [-outfeat]           featout    File for output features

   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.

   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 standard output
   -filter              boolean    Read standard input, write 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 deaths


   Standard (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
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.checktrans
   [-outseq]
   (Parameter 3) Sequence file to hold output ORF sequences Writeable
   sequence(s) <sequence>.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 regul
ation
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.

   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').

  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 2005-07-15
##Type Protein PAAMIR_1
PAAMIR_1        checktrans      misc_feature    278     634     0.000   +
.       Sequence "PAAMIR_1.1"

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      Count 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

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
