Prediction softwares especially with respect to structure and function
ORF finder at NCBI and Ecgene are software which you can use for for the purpose.
Are you looking just for ORF or for protein coding genes ? These two things are related but different. Small ORFs are usually not considered as genes but may actually be (polypeptides). Long ORFs are usually considered as genes but may actually be not. This is especially true in GC rich genomes where the presence of STOP codons (GC poor) are usually almost absent on the opposite strand of a real gene.
Then it's better to use a real prokaryotic gene finder. Examples are Glimmer, FrameD...
See for example http://tata.toulouse.inra.fr/apps/FrameD/FD or http://www.cbcb.umd.edu/software/glimmer/
I am looking at an ORF gene that is protein coding. It is not charcterized. So am looking for some softwares that can help me gain some insight into the functional/structural aspect of the ORF. It is a human ORF (not looking into prokaryotes).
Ok. the ORF terminology is unusual for eukaryotes (for me at least). I usually hear about intronless genes. The software I mentionned are useless then :)
Nallasivam Palanisamy: Sir the ORF which I am looking into, I am aware of the protein coding regions of the ORF. I have used ORF finder but it just gives the representation of the frames within the region. It would be helpful if I could use any bioinformatics tools to predict the protein structure, function or the signaling pathways/interctome with any reliable softwares.
If you are analysing your cDNA sequence, then you can use ORF finder from NCBI, or other softwares under section Proteomics from Expasy.org. You can find many other softwares for protein structure prediction in Expasy. If you want to check for your protein localization you can use PSORT.
I have tried PSORT (Human WoLFPSORT to be specific). I have got some results out of that but am not aware regarding the reliability of the result.
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