Question: Compute a identity matrix from an alignment - command line approach for batch processing
0
gravatar for fhsantanna
3.5 years ago by
fhsantanna490
Brazil
fhsantanna490 wrote:

I have an 16S rDNA alignment in FASTA format and I want to generate an identity matrix from it. Bioedit has a tool for this purpose, however I need a command line one for batch processing. Do you know a script able of doing it?

batch identity alignment • 2.9k views
ADD COMMENTlink modified 10 months ago by gadget0 • written 3.5 years ago by fhsantanna490
1

It might be helpful if you described the problem in more detail. For example - "I have hundreds of alignments and I want to generate an identity matrix for each one of them"

This does not have the necessary information. Do you mean that you have hundreds of files? One file with lots of alignments? What is the format of your alignments? ...etc. So, please clarify.

ADD REPLYlink written 3.5 years ago by Brian Bushnell17k
2
gravatar for Michael Dondrup
3.5 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

DNA or AA? Otherwise, computing a distance matrix on MSA is a basic task in phylogenetics, done - for example - by long-existing tools:

EMBOSS: distmat

MEGA can also calculate distance matrices.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Michael Dondrup47k

Actually I need the opposite. Emboss and DNAdist calculate the distance. I just need the identity values among the sequences. I am working with rRNA 16S sequences, and their identity values are important for bacterial species identification.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by fhsantanna490

So, what do you want to calculate:

  1. For each pair, the number of identical positions
  2. the proportion of identical values (% identity)
  3. the actual sequences that are identical
ADD REPLYlink written 3.5 years ago by Michael Dondrup47k

I would like to compute the % identity.

ADD REPLYlink written 3.5 years ago by fhsantanna490
0
gravatar for gadget
10 months ago by
gadget0
gadget0 wrote:

See PIM from MUSCLE

ADD COMMENTlink written 10 months ago by gadget0
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