We have recently submitted a complete genome of an organism. I wonder if we can access and analyze pathways for the organism. I tried searching several GI and Genbank Accession Numbers into the DAVID or KEGG database, however, they cannot recognize my submission. Any tips on how to analyze this RECENTLY uploaded genome?
The KEGG database provides you with a powerful tool called KAAS (KEGG Automated Annotation Server). There you can upload your fasta sequences from a multifasta file, not one by one. The KAAS will perform a homology search to assign a K number to those sequences that have a significant hit to any of the manually curated genes contained in the database. The output file will be a list with your genes' ID and its respective K number whenever they were annotated. You can use the K number list to generate a visual representation of metabolic or signaling pathways for your data.
Here is the KAAS link: http://www.genome.jp/tools/kaas/ in case you want to give it a try.
It takes time for KEGG to perform metabolomic annotation of new sequenced genomes. Meanwhile you can proceed your project in a way that if you had performed complete conceptual translation of your genome then search homology of your proteins in KEGG database. For every good homology (say 80% or above), it can be assumed that your protein belonged to the pathway to which 'best hit' belonged to. By using some programming magic, you can search it in a single go. Try to restrict your homology search closest to your organism taxonomy.
HTH.
There's a tool in KEGG called BlastKOALA. The input to this tool is the predicted protein sequences of the new genome. The tool gives an output of reconstructed pathways based on Blast homology of the KEGG database. The only issue with this tool is you cannot change the parameters of blast, have to go with the defaults.
Thank you so much, sirs! But it seems a laborious work to one by one search each protein. I want to do a fully automated search and annotation, and then produce an image for the pathways.
Dr. Sufian, how long does it take for KEGG to perform metabolic annotation of newly uploaded genomes? I am using a different software to tap into the KEGG database but if the KEGG doesn't recognize the genome yet. It seems worthless at this moment.
Thanks for your comments. Any other suggestions?
The KEGG database provides you with a powerful tool called KAAS (KEGG Automated Annotation Server). There you can upload your fasta sequences from a multifasta file, not one by one. The KAAS will perform a homology search to assign a K number to those sequences that have a significant hit to any of the manually curated genes contained in the database. The output file will be a list with your genes' ID and its respective K number whenever they were annotated. You can use the K number list to generate a visual representation of metabolic or signaling pathways for your data.
Here is the KAAS link: http://www.genome.jp/tools/kaas/ in case you want to give it a try.
Mr. Pajarillo, KAAS is a better option for metabolic pathway annotation. Let us know about your progress.
Thanks guys! It's a very good and fast annotation program using KEGG orthology! It works. But I am wondering, will my content be publicly seen already? Or is it just me who can access it?
It is private and will be stored for 7 days, enough time for you to download your annotation list. Once you have your list, you can map it (whole or in parts) anytime with the KEGG mappper by providing the KO terms: http://www.genome.jp/kegg/tool/map_pathway.html
Good to know the KAAS worked great with your data!
For pathway analysis It is best to upload your genome at RAST server .
which will give the what all subsysems present in your genome and its higher level processes.
you can also compare your genome with other genomes of interest at pathways level.
link to access RAST : http://rast.nmpdr.org/
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