Confirming Sequences In Specific Regions Of Interest

Question

[Cacau]

Hi all,

I am considering using raw sequencing data available online to demonstrate the existence of a specific sequence of interest in a bacterial genome. This sequence is special and has tandem duplications based on genome sequence available. How should I use raw sequencing data online to reanalyze it to make sure that the sequence does exist in the genome? Do I need to reassemble the region of interest? If the answer is YES, should I use a reference based strategy or de novo strategy (this duplication does not exist in other genomes). Thanks a lot!

Answer 1

[ancient_learner]

what I understood from your question is you have a sequence of your interest and you want to see whether it exists in the some bacterial genome. you didn't mention which format it is in (fasta/fastq/sam etc)

1) If you have a single sequence of interest: to check whether your sequence is really present (if yes where) you will have to use Alignment programs (like Blast) In this case If your sequence is present specifically in your bacterial strain it should be able to show that

2) If you have multiple reads use bowtie like softwares

use a reference based strategy first to make sure that the sequence does exist in the genome

[Cacau]

Thanks! I think I did not mention my question very clearly. What I want to see is whether the gene of interest does exist in the a bacterial genome. Also the genome that has been already released shows the existence of the gene, I guess it might be due to mis-assembly. So I want to reassemble the genome sequence to see whether it does exist there.

Answer 2

[Rayan Chikhi]

Sounds like a task for which Mapsembler was made. The publication has examples of assembly around regions of interest.

Just be sure to input a short, well-conserved part of your sequence of interest (~ 100 bp).

[Cacau]

Thanks so much! It seems this software can be very helpful in my study!