How To Blast Consensus Sequences With Bacterial Genome?

Question

[Raghav]

Dear all,

Subject- To find number of hits available for the particular consensus sequence in bacterial genome

I am having this consensus sequence

GAAUGUCUUCGGGGCAGGGUGAGGAGRGNNNNNNNNNNNNHNCVGGGNNNUGGUGNNNNNNNNNNNCNDNNGNDNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNYNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNRYSYDRRRNNNNNNNNNNNNNNNNNNUNNNANNCNCGNNNVCCRACVGUNNNANNNVBDNNBAUKYUHNNDNNYNNVNNBNNNVAGUCNGGAUGKNNANDNNNNNNNNNNNDRGGAGAAGGAGGCA

i need to perform an online BLAST with a bacterial genome. Don't know how to do it

[always_learning]

Why you want to do only online blast ? What are numbers of genomes ? But I will suggest you for below: 1) Install the Blast 2) Download the Bacterial Genome 3) Run blast for query sequence with Genome.

Answer 1

[Manu Prestat]

Online NCBI Blast lets you choose (or exclude) organisms. However, I would investigate a bit to see how BLASTN (or megablast which is the default) handles the numerous Ns you got.