checktrans

 

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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:6.5.0.0

   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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)
seqall Protein sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required
-orfml integer Minimum ORF Length to report Integer 1 or more 100
[-outfile]
(Parameter 2)
outfile Output file name Output file <*>.checktrans
[-outseq]
(Parameter 3)
seqoutall Sequence file to hold output ORF sequences Writeable sequence(s) <*>.format
[-outfeat]
(Parameter 4)
featout File for output features Writeable feature table unknown.gff
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. Boolean value Yes/No Yes
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1
-sbegin_sequence
integer Start of each sequence to be used Any integer value 0
-send1
-send_sequence
integer End of each sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence
boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence
boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence
boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence
boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence
boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence
boolean Make upper case Boolean value Yes/No N
-scircular1
-scircular_sequence
boolean Sequence is circular Boolean value Yes/No N
-sformat1
-sformat_sequence
string Input sequence format Any string  
-iquery1
-iquery_sequence
string Input query fields or ID list Any string  
-ioffset1
-ioffset_sequence
integer Input start position offset Any integer value 0
-sdbname1
-sdbname_sequence
string Database name Any string  
-sid1
-sid_sequence
string Entryname Any string  
-ufo1
-ufo_sequence
string UFO features Any string  
-fformat1
-fformat_sequence
string Features format Any string  
-fopenfile1
-fopenfile_sequence
string Features file name Any string  
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile
string Output directory Any string  
"-outseq" associated seqoutall qualifiers
-osformat3
-osformat_outseq
string Output seq format Any string  
-osextension3
-osextension_outseq
string File name extension Any string  
-osname3
-osname_outseq
string Base file name Any string  
-osdirectory3
-osdirectory_outseq
string Output directory Any string  
-osdbname3
-osdbname_outseq
string Database name to add Any string  
-ossingle3
-ossingle_outseq
boolean Separate file for each entry Boolean value Yes/No N
-oufo3
-oufo_outseq
string UFO features Any string  
-offormat3
-offormat_outseq
string Features format Any string  
-ofname3
-ofname_outseq
string Features file name Any string  
-ofdirectory3
-ofdirectory_outseq
string Output directory Any string  
"-outfeat" associated featout qualifiers
-offormat4
-offormat_outfeat
string Output feature format Any string  
-ofopenfile4
-ofopenfile_outfeat
string Features file name Any string  
-ofextension4
-ofextension_outfeat
string File name extension Any string  
-ofdirectory4
-ofdirectory_outfeat
string Output directory Any string  
-ofname4
-ofname_outfeat
string Base file name Any string  
-ofsingle4
-ofsingle_outfeat
boolean Separate file for each entry Boolean value Yes/No N
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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 3
##sequence-region PAAMIR_1 1 634
#!Date 2012-07-15
#!Type Protein
#!Source-version EMBOSS 6.5.0.0
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 © 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 © 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