| Name |
CHECKTRANS |
 |
| Status |
The current release has 0
entries and was indexed 06-Sep-2004.
|
| Creation date |
Completed 24 Feb 2000 - Rodrigo Lopez Rewritten 2 March 2000 - Gary Williams
|
| Description |
CHECKTRANS application details page
Reports STOP codons and ORF statistics of a protein
Reads in a protein sequence containing stops, and writes a report of anyopen reading frames (continuous protein sequence with no stops) that aregreater than a minimum size. The default minimum ORF size is 100residues. 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 togive checktrans translations in all three (six?) frames in orderfor it to be effective at finding all possible ORFs.
|
| Literature |
None.
|
| WWW |
www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/checktrans.html
|
| Ftp |
The latest version of the EMBOSS package is available on
ftp://ftp.uk.embnet.org/pub/EMBOSS/
|
| Contact |
This application was written by Rodrigo Lopez (rls@ebi.ac.uk) EuropeanBioinformatics Institute, Wellcome Trust Genome Campus, Hinxton,Cambridge, CB10 1SD, UK. It was rewritten by Gary Williams(gwilliam@hgmp.mrc.ac.uk)to outputthe sequence data to a single file in the conventional EMBOSS style.
|
| See also |
|
BACKTRANSEQ
| Back translate a protein sequence
| |
CHARGE
| Protein charge plot
| |
COMPSEQP
| Counts the composition of dimer/trimer/etc words in a sequence
| |
FREAKP
| Residue/base frequency table or plot
| |
GETORF
| Finds and extracts open reading frames (ORFs)
| |
IEP
| Calculates the isoelectric point of a protein
| |
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
| |
PLOTORF
| Plot potential open reading frames
| |
SHOWSEQP
| Display a sequence with features, translation etc..
| |
TRANSEQ
| Translate nucleic acid sequences
|
|
|
|
| Data-fields in SRS |
|
| Loaders |
|
| SRS Description |
Structure
(
srsgen.i
,
srsdb.i
,
href.i
)
Syntax
Information
|