                                 checktrans



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Report 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
Report 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

Report STOP codons and ORF statistics of a protein
Version: EMBOSS:6.5.6.0

   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
   -scircular1         boolean    Sequence is circular
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 and exit. 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
   -version            boolean    Report version number and exit


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 regula
tion
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 3
##sequence-region PAAMIR_1 1 634
#!Date 2012-07-15
#!Type Protein
#!Source-version EMBOSS 6.5.6.0
PAAMIR_1        checktrans      polypeptide_region      278     634     .
.       .       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

   Program name     Description
   backtranambig    Back-translate a protein sequence to ambiguous nucleotide
                    sequence
   backtranseq      Back-translate a protein sequence to a nucleotide sequence
   coderet          Extract CDS, mRNA and translations from feature tables
   getorf           Find and extract open reading frames (ORFs)
   marscan          Find matrix/scaffold recognition (MRS) signatures in DNA
                    sequences
   plotorf          Plot potential open reading frames in a nucleotide sequence
   prettyseq        Write a nucleotide sequence and its translation to file
   remap            Display restriction enzyme binding sites in a nucleotide sequence
   showorf          Display a nucleotide sequence and translation in pretty format
   showseq          Display sequences with features in pretty format
   sixpack          Display a DNA sequence with 6-frame translation and ORFs
   syco             Draw synonymous codon usage statistic plot for a nucleotide
                    sequence
   tcode            Identify protein-coding regions using Fickett TESTCODE statistic
   transeq          Translate nucleic acid sequences
   wobble           Plot third base position variability in a nucleotide sequence

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 (c) emboss.open-bio.org) not to the original author. and
   modified to output the sequence data to a single file in the
   conventional EMBOSS style 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 (c) emboss.open-bio.org) not to the original author.

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
