strand bias, gram negative bacteria

Question

[Nitha]

Hi All,

I have some doubts in strand bias calculation.

Generally it’s said, that in prokaryotes (bacteria) that majority of highly expressed genes are located in Leading strand and these genes are taken further analysis. I am trying to check codon bias and strand bias for my bacteria, but unfortunately when i checked strand bias with CAI-value greater than 0.65 for my organism the most highly expressed gene (ribosomal gene) are present in lagging strand.. so I am confused how to deal in such situations..

what gene should I consider? what this higly expressed gene in lagging strand gene inform? How to check strand bias for bacteria?

It will be help full if u guys give me some idea..

Thanks,

Answer 1

[natasha.sernova]

Strand bias:

A lot of theory:

http://www.ncbi.nlm.nih.gov/pubmed/12847524

http://www.sciencedirect.com/science/article/pii/S167202291200037X

http://www.intechopen.com/books/dna-replication-current-advances/strand-specific-composition-bias-in-bacterial-genomes

http://nar.oxfordjournals.org/content/33/10/3224.full

These authors showed how to calculate the bias.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458553/

http://www.nature.com/articles/srep16431

Hopefully it will help you.

[Nitha]

Thanks! its helpful.