local blast and provide taxonomy to the querry

Question

[shashank.gupta]

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

[Bioinformatics_NewComer]

Do you've sequences from 16S data?

[shashank.gupta]

Yes. this is from 16S data

[Bioinformatics_NewComer]

Great. Why not use RDP classifier?

[shashank.gupta]

I hope that works. thanks

[st.ph.n]

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.