IMTECH
INSTITUTE OF MICROBIAL TECHNOLOGY
BIOINFORMATICS CENTER
GENEBENCH: EVALUATION OF GENE FINDERS AND DATASET CREATION SERVER




Missed genes:- Number of genes that are completely missed by the gene finders; Sen-Nucleotide Level Sensitivity; Spe-Nucleotide Level Specificity; AC-Approximate Correlation; CC-Correlation Coefficient; CR-Proportion of correctly predicted exons; PC-Proportion of predicted exon whose one end is correctly predicted; OL-Proportion of predicted exons whose both end are incorrect but overlaps an actual exon; ME-Proportion of actual exons that are missed by the program; WE-Proportion of predicted exons that do not overlap an actual protein-coding exon; ESn-Exon Level Sensitivity; ESp-Exon Level Specificity; EAvg-Average of Sensitivity and Specificity at exon level; GSen-Gene Level Sensitivity; and GSpe-Gene Level Specificity. Number in bracket indicate the number of exons in each category.


Results from ab initio programs on HMR195 dataset: Click here for evaluation criteria

Programs Number
of
Missed Genes 		NUCLEOTIDE LEVEL ACCURACY EXON LEVEL ACCURACY GENE LEVEL ACCURACY
Sen Spe AC CC CR PC OL ME WE ESn ESp EAvg GSen GSpe
GENSCAN 3 0.93 0.89 0.91 0.89 0.69 (735) 0.19 (131) 0.02 (10) 0.08 -(76) 0.09 (104) 0.70 0.69 0.70 0.37 0.35
HMMgene 5 0.90 0.90 0.91 0.89 0.75 (715) 0.14 -(98) 0.02 (11) 0.12 (128) 0.07 -(81) 0.74 0.75 0.75 0.46 0.46
Results from ab initio on Burset/Guigo dataset: Click here for evaluation criteria

Programs Number
of
Missed Genes 		NUCLEOTIDE LEVEL ACCURACY EXON LEVEL ACCURACY GENE LEVEL ACCURACY
Sen Spe AC CC CR PC OL ME WE ESn ESp EAvg GSen GSpe
GENSCAN 8 0.93 0.91 0.92 0.90 0.79 (2156) 0.13 (264) 0.02 (26) 0.09 (203) 0.05 (188) 0.78 0.79 0.79 0.45 0.44
HMMgene 38 0.87 0.88 0.91 0.86 0.77 (2092) 0.11 (239) 0.01 (21) 0.14 (308) 0.04 (139) 0.76 0.77 0.77 0.51 0.50




Results from combination of ab initio programs on HMR195 dataset: Click here for evaluation criteria

Programs Number
of
Missed Genes 		NUCLEOTIDE LEVEL ACCURACY EXON LEVEL ACCURACY GENE LEVEL ACCURACY
Sen Spe AC CC CR PC OL ME WE ESn ESp EAvg GSen GSpe
EUI 3 0.92 0.94 0.93 0.91 0.81 (769) 0.13 (74) 0.01 (4) 0.10 (104) 0.04 (55) 0.77 0.81 0.79 - -
EUI-FRAME 3 0.92 0.94 0.93 0.91 0.82 (762) 0.13 (70) 0.01 (5) 0.11 (115) 0.03 (46) 0.77 0.82 0.79 - -
GI 15 0.84 0.89 0.90 0.84 0.80 (742) 0.09 (57) 0.01 (3) 0.19 (149) 0.03 (43) 0.72 0.80 0.76 - -
Results from combination of ab initio programs on Burset/Guigo dataset: Click here for evaluation criteria

Programs Number
of
Missed Genes 		NUCLEOTIDE LEVEL ACCURACY EXON LEVEL ACCURACY GENE LEVEL ACCURACY
Sen Spe AC CC CR PC OL ME WE ESn ESp EAvg GSen GSpe
EUI 20 0.90 0.92 0.93 0.90 0.84 (2214) 0.09 (176) 0.01 (12) 0.12 (250) 0.03 (98) 0.80 0.84 0.82 - -
EUI-FRAME 27 0.88 0.92 0.92 0.88 0.84 (2188) 0.08 (167) 0.01 (11) 0.13 (286) 0.03 (87) 0.79 0.84 0.81 - -
GI 43 0.84 0.90 0.91 0.85 0.83 (2118) 0.07 (138) 0.01 (8) 0.18 (387) 0.02 (67) 0.76 0.83 0.80 - -




Results from combination of ab initio and similarity based approach programs on HMR195 dataset: Click here for evaluation criteria

Programs Number
of
Missed Genes 		NUCLEOTIDE LEVEL ACCURACY EXON LEVEL ACCURACY GENE LEVEL ACCURACY
Sen Spe AC CC CR PC OL ME WE ESn ESp EAvg GSen GSpe
GENOMESCAN 1 0.96 0.87 0.91 0.90 0.71 (781) 0.13 (115) 0.02 (16) 0.05 (45) 0.14 (213) 0.78 0.71 0.74 - -