KEGG Tutorial: KAAS job requesting

KAAS is the annotation platform using KEGG databases. It allows the public to match their own source of organism's dataset against the KEGG pathway gene databases.

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There are a few considerations during the input of KAAS job:

1.  Search program (BLAST, GHOSTX or GHOSTZ)

In general, the accuracy of the search programs is:

BLAST > GHOSTX > GHOSTZ

But their consumed time is in reverse order (GHOSTX is about 100 times and GHOSTZ is about 200 times more efficient than BLAST). 

2. Query sequence types (nucleotide or protein)

KAAS accepts both the nucleotide and protein FASTA files. However, the only concern is the size of the file, together with the size of the sequences in selected organisms (that you would like to BLAST against).

For amino acid sequence queries:
(the number of query sequences) * (the total number of sequences in selected organisms) < 135,000,000,000

For nucleotide sequence queries:
(the number of query sequences) * (the total number of sequences in selected organisms) < 135,000,000,000 / 3

3. GENES data set 

This is up to your preference regarding which organisms of KEGG dataset would be included in KAAS run. Only up to 40 organisms are allowed.

4. Assignment method: BBH or SBH method

If your source of dataset is from a complete set of genes in a genome is known and available in public, (for example: Olyza sativa subsp. japanica (Rice), Arabidopsis thaliana), then you may choose BBH (bi-directional best hit) method.

If your source of dataset has only a limited number of genes reported in the public databases, you may choose SBH (single-directional best hit) method. 

The difference between the two methods is as seen literally. BBH method (also known as reciprocal best hit or reciprocal Blast hit) would only assign those genes that bi-directionally matches with the KEGG databases, and thus it takes about twice as much as that of SBH-based method.

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After all the selection, you could just fill your email address and click "compute".

Please note that you have to verify your job request in your email (normally receive within 5 min), and it will take around 24 hours for the server to complete the job, and they will notify you by email.

Thank you for reading. Happy KAAS job requesting!