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Microbial Genomic BLAST

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?

genome
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updated by h.mon h.mon • written by arghya1611 • arghya1611

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

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written by GenoMax GenoMax

1 answer

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.

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written by h.mon h.mon

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