Analysis with Cazyme database

[sumitra]

Hi Daniel,

I’ve got blast output after performing blastx of my sequences against Cazy database
This is how the output looks:

I would like to import this blast.tab output into Megan and visualize the functional entities on EC. But I am not sure which mapping file I should use as CAZY has got its own mapping file
https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam.subfam.ec.txt

So im confused on which mapping file to use, should I use CAZY mapping file or megan-map-Jul2020-2-X.db.zip? Will I be able to get visualize both the enzyme family and class on EC?

Thank you

[Daniel]

Did you try megan-map-Feb2022.db.zip? That contains mappings of accessions to EC numbers.

@sumitra

I would like to import this blast.tab output into Megan and visualize the functional entities on EC. But I am not sure which mapping file I should use as CAZY has got its own mapping file
https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam.subfam.ec.txt

That mapping won’t work straight out of the box because MEGAN uses single integers as IDs.

For example, the CAZY mapping file shows:

AA2 NP_001237785.1 1.11.1.11

Opening a MEGAN mapping file with sqlite3, you can see how this is represented there:

sqlite3 megan-map-Jan2021-ue.db
SQLite version 3.26.0 2018-12-01 12:34:55
Enter “.help” for usage hints.
sqlite> select EC from mappings where Accession=“NP_001237785”;
111010011

If numbers is an array containing the EC numbers, I use the following calculation:

id = 100 * 100 * 10000 * numbers[0] + 100 * 10000 * numbers[1] + 10000 * numbers[2] + numbers[3]

So, if you want to create your own mapping of accessions to EC ids used by MEGAN, apply this formula.