Hello Krunal, 

As Pritam told you PASA and Ensembl are good options.

You can also check out this site http://molbiol-tools.ca/Genomics.htm

It could help :)

Use Augustus

thanks guys ......

well i started using cegma i hope it will give me good results.

with Auustus i am not be able to prepare training sets ...any guidence?? 

Through FISH

Prokka tools is the best one to detect a novel gene, since it will detect based on the characteristic of a gene initial and end codons and other group of set characteristics. Use this for a novel gene identification, even using other tools can do, but it will provide more than others.

Nandaggopal Murugan thanks but i am looking for Eukaryotic..... 

Ok good

Have you tried GlimmerHMM?

http://ccb.jhu.edu/software/glimmerhmm/