New FGENESH HMM based Gene Prediction program from CGG

Victor Solovyev solovyev at sanger.ac.uk
Fri Jan 29 06:36:10 EST 1999


We installed New gene-finding HMM based program FGENESH
 for multiple gene prediction in human (mammalian) genomic DNA
   It shows superior accuracy of gene prediction
                (Salamov A.A, Solovyev V.V, 1999)

Very important feature!!!! If we take the subset of exons predicted by
Fgenes and Fgenesh (programs using very different approaches)
for long genomic sequences or sequences with multiple genes,
 then the observed specificity is 95% and this set will include about
76% of all real exons. These predictions will provide positional
cloners, gene hunters and others with the best exon candidates observed
in finished and unfinished genomic sequences.

It is available at http://genomic.sanger.ac.uk/ of our
Computational Genomic Group WEB server
(http://genomic.sanger.ac.uk/gf/gf.html)

Accuracy of gene-finding programs for 1.4 MB genomic region on human chromosome
13q
=================================================================================
*** accuracy data provided by Tim Habburd and Richard Briskevich (the Sanger
Centre)
as a blind test for difficult genomic region

acc -is specificity (true predicted/all predicted) cov is sensitivity (true
predicted/true)

NE - number of predicted exons

Region includes 159 true exons
			               exact match  overlap exons   5'-exons
     3'-exons
			 NE           N  acc  cov    N  acc  cov    N  acc  cov
   N  acc  cov
fgenesh.masked          169         110 0.65 0.69  125 0.74 0.79  118 0.70 0.74
  116 0.69 0.73
fgenesh	                190         109 0.57 0.69  126 0.66 0.79  117 0.62 0.74
  117 0.62 0.74
fgenes.masked           238         103 0.43 0.65  132 0.55 0.83  114 0.48 0.72
  118 0.50 0.74
fgenes                  281         104 0.37 0.65  136 0.48 0.86  116 0.41 0.73
  120 0.43 0.75
genscan	                292         105 0.36 0.66  129 0.44 0.81  116 0.40 0.73
  115 0.39 0.72
fgeneh                  381          68 0.18 0.43  101 0.27 0.64   79 0.21 0.50
   87 0.23 0.55
mzef                    623          95 0.15 0.60  122 0.20 0.77  106 0.17 0.67
  107 0.17 0.67

***

-- 
Victor Solovyev
The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK
Email: solovyev at sanger.ac.uk  http://genomic.sanger.ac.uk
Phone: 44-1223-494799  FAX:   44-1223-494919




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