How do I determine what genes are in my area of interest?

Question

[MalloryHazel83]

Hello there,

I am new to Bioinformatics, and I am unsure as to:

1. I should locate genes in an area of interest?
2. Determine what strain of E. coli that I may have?

The area of interest is called the LEE region in E. coli (determined by using the Center for Genomic Epidemiology webapge). I have done whole genome sequencing with this organism and obtained 6 contigs. The LEE area is in the first contig in the position between about 1 758 848 to about 1 790 939.

The assembly was done with SPADES and the annotation with PROKKA.

Thank you in advance,

Mallory

[GenoMax]

If you have done annotation with PROKKA don't you have information about what genes there are on your contigs? Have you done alignments using the LEE regions sequence against your contigs? Do you see any similarities? Since the region you are interested in is about 30kb+ you may want to try alignments with Mauve to see if you can locate that regions in your contigs.