create sequence similarity network directly from FASTA file

Question

[taojincs]

Hi everyone, I am looking for an open-source software that I can incorporate into Django or any existing tool to create sequence similarity network from FASTA file.

Given several protein sequences in fasta format, it will create a network of sequence similarity with each sequence labeled.

I looked into visone and EFI - Enzyme Similarity Tool and hope to learn more great tools.

I basically want to create protein similarity network among some (10-20) selected proteins within the same homologous clusters. Is there a more efficient way/existing open-source tool so that I can incorporate it into my website development?

Thank you a lot.

Answer 1

[Mensur Dlakic]

Comparing all sequences against each other using BLAST will give you a numerical representation of sequence similarity. Those can be fed into MCL which will produce clusters, and clusters are easy to convert into networks.