thanks for the kind suggestion. i have tried EggNOG its good but is not giving any visual or graphical representation of the output. further its not summarizing the results in different categories like in biological process and cellular compartments etc. is there any tool that could give me graphical representation of the results too...?? or where i could use the results of EggNOG graphically???
im already using BlastQuala with KEGG pathways. its good but i want to analyze resulta with moree than one software for comparative analysis too.
further I do have GO (Gene ontology) and KO (KEGG) annotations for my gene but could not figure out how to use these annotation in gene ontology site or PANTHER for funtional analaysis prediction??? any idea about it???
not sure what you mean by this "the softwares like GO database VLad etc are providing functional analysis only for the geneome that are well annotated" but to find gene functions you need well annotated references and yes mostly it are model organisms.
I mean to annotate your genome in these softwares you need to select the organism in the predefined list while my organism is not listed there hence i cannot use these softwares. im using KEGG database based BlastQUALA where i dont need any reference genome to assess functional annotation of my genes. I only need fasta format of the protein sequences and simply have to paste to get results.
looking some sort of similar software to get more comprehensive and comparative results.
Ah, like that. Good explanation. I think you will need to blast or something like that and dig trough the hits. Connection the id's of different databases to functionalities. Still think that eggnog, gene ontology and maybe Panther are the best options. I don't know if there is a tool that can do all the steps for you. You need to make a sort of a pipeline. Maybe you can let know if the answers are useful or not so other people can also help you.