Question: Quantify similarity between multi-fasta files
gravatar for rowe
5.3 years ago by
United Kingdom
rowe0 wrote:

Hi there,

I want to compare the output of de novo assemblies of multiple samples. From this, I'd like to cluster the samples on (dis)similarity.

With bla(s)t, I get per-sequences scores (which I could use to get a percentage of similar bases between the query and database). With CD-HIT (EST), I do get clusters, but still no score/percentage.

Does anybody have a more straightforward solution for this?

Seasons greetings,


ADD COMMENTlink modified 5.3 years ago by learnBioinformatics40 • written 5.3 years ago by rowe0
gravatar for learnBioinformatics
5.3 years ago by
United States
learnBioinformatics40 wrote:

If I remember right, clustalW can give the similarity matrix between sequences.

ADD COMMENTlink written 5.3 years ago by learnBioinformatics40
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