Microbial Genomic BLAST

Question

[arghya1611]

Hi I have a draft bacterial genome sequence which i would like to BLAST in its entirety i.e. using the whole genome to find the nearest neighbor. NCBI offers a Microbial genome BLAST, however, since the genome is in contigs, each contig gives a similar but non-identical closest neighbor. Can anyone suggest what is the way to address the problem here?

[GenoMax]

How many contigs are we looking at? Do you know what this genome is similar to? Perhaps you could use mauve.

Answer 1

[h.mon]

It is not a problem, it is a feature, both biological and algorithmic. Maybe what you want is some phylogenomic method? See this and this papers for suggestions of phylogenomic methods, but there are several others, e.g. AMPHORA.