BLAST

Question

[m90]

hello everyone,

i have 10 Fasta files , including many DNA sequencing from different species and i want to do a blast . to see each sequence i have belong to which species , how i can do this with local blast because i want use ncbi database to align the sequences against it ?

[GenoMax]

What kind of hardware do you have access to? While you know what you need to do, it may be important to understand what that requires in terms of hardware. Blasting against nt (large db) requires significant amount of RAM/storage.

Have you considered using a program like kraken2 that can help classify reads?

[m90]

i will use ubuntu , i have conda so , i wii download blast , but i dont know in -db part will write ncbi or what ? beacuse i always use private database , so if you have code just share it and i didnt use kraken2 before.

[GenoMax]

NCBI's command line blast is described in this handbook: https://www.ncbi.nlm.nih.gov/books/NBK569856/

You can use -remote option with command line blast+ to directly search some of the databases at NCBI via their web option.

If you want to do the search locally then you will need to download the pre-formatted databases from https://ftp.ncbi.nih.gov/blast/db/ . Depending on the database you choose you may need to have tens of GB of RAM and hundreds of GB of storage locally available.