gene functional analysis

Question

[blooming.daisy333]

hi all,

can someone kindly suggest me a useful tool for the functional analysis of protein data. the softwares like GO database VLad etc are providing functional analysis only for the geneome that are well annotated and are already in there database. can someone suggest me any good software that could classifies genes by their function using only IDs and fasta sequences (of protiens ) in different categories like which biological process, cell compartment etc..

thanks in anticipation

[gb]

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.

[blooming.daisy333]

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.

[gb]

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.

Answer 1

[gb]

EggNOG: http://eggnogdb.embl.de/#/app/home

Maybe also KEGG: https://www.genome.jp/kegg/pathway.html

[blooming.daisy333]

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???

[gb]

I thought panther was a database that links all the id's together they also offer a R package I think. Never used it, so you should ask skadum. Making visualizations is something else, you could post a new question about that. You can use R or python for that. https://blog.modeanalytics.com/python-data-visualization-libraries/ https://www.rstudio.com/

Summarizing the results would be a next step and also a new question for this forum. If the information is in de output you can post an example and ask how to categorize it. If you don't have the informatie try to find it and post an example of the eggnog output and your categorie output and ask how to do it.

Answer 2

[pbpanigrahi]

Tried DAVID ??

Answer 3

[skadum]

You can use Panther http://www.pantherdb.org/ or http://amp.pharm.mssm.edu/Enrichr/ and maybe you can test https://omictools.com/ site that try to group in the same portal all bioinformatic tools.

[blooming.daisy333]

thanks for the suggestions. PANTHER is very good software but the problem is that it supports only few gene ID formates like uniprot enssemble etc where my geneome annotation is not available. Gene Ontology is powered by PNTHER and 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???