Dear Friends,
I have been looking for a program or tool for genome alignment (in my case phages). I have an assembled phage and multiple genomes from BLAST hit; I annotated the genes in these phages using DNAMaster, and now, I want to align these genomes against each other and have been looking for a program with which I can view the alignment and the annotated genes something similar to this below image, where the genes are presented in a block or something that is visually distinguishable. The alignment will be used for comparative analysis to look for genes of interest among the genomes including the assembled phage.
I was using Mauve from Darling lab but it does not give result like what I am looking for; however, if you know of a way to get a presentation like this for genome alignment, please suggest me. Please let me know if something is not clear.
Thanks, DK
not exactly what you might be looking for but perhaps of some use : ACT , the artemis editor with comparative mode.
Thanks Lieven! I am trying ACT; however, I don't think ACT does genome alignment? It only performs pairwise comparison. Am I right? Any idea on a tool to do a significantly accurate genome alignment? Thanks for your time.