This is a test version of Biostars. For the public version, visit https://www.biostars.org.
local blast and provide taxonomy to the querry

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
• 2,199 views • link
updated by GenoMax GenoMax • written by shashank.gupta • shashank.gupta

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.

• 0 views • link
written by st.ph.n st.ph.n

0 answers

No answers yet.

Log in to answer this question.

More posts like this