We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains (about 200). I would like to know your suggestions to perform this step.
From my bioinformatic experience, it could be possible to start with a first rough screening using blastp or blastx against a multiple strain database, and more accurate approaches would be then performed to validate this results.
Please let me know your suggestions and possible references you might consider helpful to answer this question.
Thanks for your help. Best regards, Bernardo