Question: Amino Acid matrices freely downloadable url
gravatar for RT!37
3 days ago by
RT!370 wrote:

Any resource to d freely download Amino Acid matrices : VTML, OPTIMA, MD, RBLOSUM.

Reference articles do not have such urls or it`s not working!!

Thanks !!

alignment sequence • 136 views
ADD COMMENTlink modified 2 days ago by pevsner420 • written 3 days ago by RT!370
gravatar for pevsner
2 days ago by
Kennedy Krieger Institute (Baltimore, MD)
pevsner420 wrote:

Here's a place to download PAM and BLOSUM matrices (and Dayhoff, GONNETT):

Jones matrices are here:

RBLOSUM62 and RBLOSUM64 are given here as a PDF:

The VTML200 matrix is given here:

PFASUM matrices are available here (via PDF and tar.gz) from the project website:

OPTIMA matrix is given as a PDF in Kann M, Qian B, Goldstein RA. Optimization of a new score function for the detection of remote homologs. Proteins. 2000 Dec 1;41(4):498-503. PubMed PMID: 11056037.

ADD COMMENTlink written 2 days ago by pevsner420

Thanks ... !! Similar to BLOSUM and PAM, does we have any resource for VTML series of matrices ??

ADD REPLYlink written 2 days ago by RT!370

See the link POP. You can also find some references and original scripts to generate the matrix there.

ADD REPLYlink written 17 hours ago by doctor.dee005170
gravatar for doctor.dee005
2 days ago by
Bioinformatics Center, Pune
doctor.dee005170 wrote:

BLOSUM and PAM series matrices are available on NCBI ftp. See this link:

ADD COMMENTlink modified 17 hours ago • written 2 days ago by doctor.dee005170
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1523 users visited in the last hour