local blast and provide taxonomy to the querry
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7.2 years ago

Hi,

I have a local database, and querry sequences (~500 sequences), I need to blast 500 sequences to local database and provide taxonomic information to all the 500 sequences.

Local database looks like -

>AB005893.1.1549 Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;Lactobacillus collinoides TACGTAGGTGGCAAGCGTTGTAAAAAAATTT.....................
>AB005893.1.1549 Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae TACGTAGGTGGCAAGCGTTGTCCCCCCCC..........................

and so on...

and querry sequences -

>ABC_1
TACGTAGGTGGCAAGCGTTGTCCCCCCCC
>ABC_2
TACGTAGGTGGCAAGCGTTGTGGGGGG
>ABC_3
TACGTAGGTGGCAAGCGTTGTAAAAAAATTT

perform blast against a local database and similarity percentage minimum 97% and gives the taxonomy to query

Desirable output should be like -

>Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae
TACGTAGGTGGCAAGCGTTGTCCCCCCCC
>Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;Lactobacillus collinoides
TACGTAGGTGGCAAGCGTTGTAAAAAAATTT
sequencing alignment blast • 1.6k views
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Do you've sequences from 16S data?

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Yes. this is from 16S data

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Great. Why not use RDP classifier?

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I hope that works. thanks

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You will have to parse your database fasta, after you get your blast results. So, for each query, grab the taxonomic information from the best matching db hit.

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