Why FgenesH and Genscan don't give good results as I have predicted number of genes of Chromosome 16 which according to NCBI are 86 but the results I have obtained are 57 genes predicted by FgenesH and only 47 genes predicted by GenScan. why they have done missed predictions. Kindly help me to know the reason?
The authoritative source for these annotations is Ensembl, see: http://www.ensembl.org/Gallus_gallus/Location/Chromosome?r=16
According to this summary, Chromosome 16 contains 46 coding and 1 non-coding region, so GenScan is pretty good (and possibly used in the annotation pipeline). Most predictions have error margins, no exception gene predictions (incl. the Ensembl predictions), so some variation is normal. Where could the additional genes in NCBI come from? Other predictions, redundant sequences, you maybe mixed up transcripts, proteins with genes, different gene build? Without the exact query it is impossible to say. So: tl;dr: Everything's fine.
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I need answer please anyone help me to solve my problem
What species are you studying?
Sorry I did not mentioned it I am studying Chicken Chromosome 16