How does GrailEXP compare to other tools?
It is difficult to compare GrailEXP to other tools because the sheer scope of what it does exceeds that of many programs to which it is compared. As far as raw exon prediction goes, Grail 1.3 performs slightly worse than Genscan on human and mouse. However, the addition of similarity search information causes GrailEXP to outperform Genscan consistently. Genscan is particularly weak in predicting the beginning and end of genes. GrailEXP vastly outperforms Genscan in regions of EST/cDNA similarity. Where there is partial EST information, GrailEXP also outperforms Genscan. In regions where there is no similarity with known genes, Genscan predicts exon edges slightly better than GrailEXP, but GrailEXP still predicts gene begin and end better. In such regions, Genscan’s tendency is to create genes that are too long; GrailEXP tends to produce genes that are too short (i.e. it breaks genes). Regardless, Genscan exons can be fed to GrailEXP’s alignment program, effectively creating a GenscanEX
