20 September

1.) Unable to find the small RNA database for strain 14028. Unable to find genome for strain ST4/74.

2.) Because of the above reasons, chose to go with the strain SL1344. Downloaded the FASTA sequence
from NCBI website. ( https://www.ncbi.nlm.nih.gov/nuccore/FQ312003 )

3.) Used the co-ordinates of the sRNA’s of SL1344 to extract the sequence from the genome.

4.) Got the sequences in an excel file.

27 September
1.) We got the RNA sequences last time. We got the reverse complements of the sequences lying on the
+ strand.

2.) Now we have to align these RNA sequences with the query sequence of the original file to check for
local alignment. The alignment can be of two types.

A.) If the sRNA binds to the query sequence, there may be gaps because of RNA folding and it
will lead to translational regulation.

B.) We need to compare the sRNA sequence to 14028 strain because technically it is a part of
that organism. So we align and see if the binding is happening at intergenic region or not.

Our ultimate goal is to check the presence / absence of intergenic regions.

17 October
1.)