For KEGG pathway analysis, use the KAAS-KEGG automatic annotation server (http://www.genome.jp/tools/kaas/) and for gene enrichment analysis, you can use GSEA (http://software.broadinstitute.org/gsea/index.jsp) or DAVID (https://david.ncifcrf.gov/)

Hope these help

thanks a lot for your answer. but the specie (olive flounder)i am working on is not a model organism so there isn't any annotation for its gene, that is why i was thinking to use blast to annotate the gene after that i will do the GO enrichment analysis and KEGG pathway analysis.

Hello Adham, 

Blast2GO already supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim.  So it looks like you can perform all of your analysis just by using it.

thanks a lot for your help guys. so what i did is using the blast2go to do the GO enrichment analysis and for KEGG i used the KAAS-KEGG using the fatsa file of my genes.

You can have a look at here too: 

amp.pharm.mssm.edu/Enrichr/enrich

Just upload your gene list and find enrichment from different knowledge-bases including KEGG too..  

hi @Ruhshan Ahmed Abir, the URL you mentioned above says expired.

You can use KASS KEGG genome analysis tool

I have tried KAAS by submitting 1k sequences, but it gave result for only 130 sequences (as provided in the result pathway list). And also it didn't showed which of my query seq belong to which of the respective pathway.

It just shows like the following -

00010 Glycolysis / Gluconeogenesis (2)

00020 Citrate cycle (TCA cycle) (1)

00040 Pentose and glucuronate interconversions (1)

00052 Galactose metabolism (1)

00053 Ascorbate and aldarate metabolism (1)

and in the pathway result page shows like-

ko05100 Bacterial invasion of epithelial cells (1) ko:K05755 ARPC4; actin related protein 2/3 complex, subunit 4 ko05166 Human T-cell leukemia virus 1 infection (1) ko:K11126 TERT; telomerase reverse transcriptase [EC:2.7.7.49]

ko05160 Hepatitis C (1) ko:K04354 PPP2R2; serine/threonine-protein phosphatase 2A regulatory subunit B

Any suggestion regarding this would be helpful.

thank u.

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