Question: Genome alignment with good pictorial representation of genome structure (with annotated genes)
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gravatar for DanielC
6 months ago by
DanielC90
Canada
DanielC90 wrote:

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.

image

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

ADD COMMENTlink modified 6 months ago by h.mon26k • written 6 months ago by DanielC90

not exactly what you might be looking for but perhaps of some use : ACT , the artemis editor with comparative mode.

ADD REPLYlink written 6 months ago by lieven.sterck5.5k

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.

ADD REPLYlink written 6 months ago by DanielC90
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