Hello Sneha,

I can think in two options:

1) Annotate the genes/transcriptomes that you have with Blast2GO (http://www.blast2go.com/b2ghome) and run the step to map the annotations with KEGG.

2) If you have some knowledge of command line tools, you can run a blast with Trembl/Swissprot database (http://www.uniprot.org/downloads), filter the output, create a pathologic file and finally use Pathways tools from MetaCyc (http://bioinformatics.ai.sri.com/ptools/) to create a new BioCyc database (). You can find some useful scripts at https://github.com/solgenomics/sgn-home/tree/master/aure/scripts/solcyc (We use them to create the Solanaceae BioCyc databases).

Good luck !!!

Another program that can be used to generate both KEGG and also SEED assignments is MEGAN4.

Unlike BLAST2GO, MEGAN4 will not do BLAST searches for you. MEGAN4 requires results from either a BLASTX or BLASTP search against a database. It does post-analysis on the blast results.

MEGAN4 is available here:

MEGAN 4 - MEtaGenome ANalyzer — Algorithms in Bioinformatics

http://ab.inf.uni-tuebingen.de/software/megan/

Ref: Huson, DH, Mitra, S, Weber, N, Ruscheweyh, H, and Schuster, SC (2011). Integrative analysis of environmental sequences using MEGAN4. Genome Research, 21:1552-1560.

Another resource is CAMERA: http://camera.calit2.net/

Ref: Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource (2011) Shulei Sun; Jing Chen; Weizhong Li; Ilkay Altinatas; Abel Lin; Steve Peltier; Karen Stocks; Eric E. Allen; Mark Ellisman; Jeffrey Grethe; John Wooley Nucleic Acids Research 2010; doi: 10.1093/nar/gkq1102

Camera is a web-based platform that can annotate your sequence data using KEGG and or COGs without you having to do the BLAST analysis.

BLAST2Go is good, but quicker results can be obtained using CAMERA.

Additional caveats with using BLAST2GO.

It takes time - and that could be a long time depending upon your computational resources.

It can generate extremely large files as it concatenates the blast output xml file from each sequence into a single "xml-like" text file. Since this file consists of several xml-files concatenated together, it is not an xml file. Thus utilizing the BLAST results from BLAST2GO (the concatenated xml-like file) for other programs requires post processing. This is easy enough using a standard text editor or other editing methods (command-line).

Some of the blast results often are not completely written to the concatenated "xml-like" file using Blast2Go. This is not apparent unless you inspect the complete file.

I have not been able to run BLAST2GO using the most recent JAVA upgrades that fix the much publicized security problem. I have had to use older, vulnerable versions of JAVA. Thus, you do run a risk of opening your computer or network to potential problems.