BESTORF - Prediction of potential coding fragment in EST/mRNA sequence
it is available at http://genomic.sanger.ac.uk/ of our
Computational Genomic Group WEB server
Program prepared to analyze Human (Mammalian) or Plant sequences (Arabidopsis)
(click Human or Plant button, respectively)
References: Solovyev V.V., Salamov A.A., unpublished data.
Algorithm is based on Markov chain model of coding regions and a
probabilistic model to combine it with Start codon potential.
Accuracy: Preliminary tests of mRNA and their fragments show that the
accuracy of recognition of true ORF is about 100% for typical
mRNA and is about 99% for EST fragments 500 - 800 bp containing coding
region. It should be less if we will present EST with
The program output potential CDS positions (where the Start codon is
probable) as well as the longest ORF positions (as an extention of
this CDS before the start codon). If observed Met codons are recognized as
internal, the CDS and ORF will have the same positions).
BESTORF Prediction of potential coding fragment in plant EST/mRNA
Time: Tue Feb 16 20:03:57 1999.
Seq name: Seq_name:
Length of sequence: 388
Predicted CDS 1 in +chain 1 in -chain 0
Position of predicted CDS/ORF:
G Str Feature Start End Score ORF CDS-Len Frame
1 + 1 CDSo 30 - 386 30.57 3 - 386 357 +3
Predicted protein fragment:
>BESTORF 1 1 fragment (s) 30 - 386 119 aa, chain +
The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK
Email: solovyev at sanger.ac.ukhttp://genomic.sanger.ac.uk
Phone: 44-1223-494799 FAX: 44-1223-494919