Question: What Next After Contigs?
0
gravatar for Smandape
5.5 years ago by
Smandape60
United States
Smandape60 wrote:

I have contigs from a bacterial genome sequence. I am trying to find what would be the reference for this strain or where does it belong to in the phylogenetic tree. Also, what would be a good way to stitch them together? I did BLAST with individual contigs and also with all contigs together but I am not sure if this is the correct way to determine which is the closest strain from the available ones in NCBI.

Any thoughts about how should one proceed without a reference?

ADD COMMENTlink modified 5.5 years ago by sentausa630 • written 5.5 years ago by Smandape60
1
gravatar for sentausa
5.5 years ago by
sentausa630
France
sentausa630 wrote:

Did you try to find its 16S rRNA sequence and BLAST it at NCBI? You might find a closely related bacterium that has its genome sequenced as your reference genome.

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by sentausa630
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