Question: Amino Acid matrices freely downloadable url
0
gravatar for RT!37
3 days ago by
RT!370
India
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
5
gravatar for pevsner
2 days ago by
pevsner420
Kennedy Krieger Institute (Baltimore, MD)
pevsner420 wrote:

Here's a place to download PAM and BLOSUM matrices (and Dayhoff, GONNETT): ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/

Jones matrices are here: ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blosum/JTT/

RBLOSUM62 and RBLOSUM64 are given here as a PDF: http://web.mit.edu/bamel/blosum/styczynski2007supp.pdf

The VTML200 matrix is given here: http://www.drive5.com/pop/VTML200I

PFASUM matrices are available here (via PDF and tar.gz) from the project website: http://www.cbs.tu-darmstadt.de/PFASUM/

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
1

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
3
gravatar for doctor.dee005
2 days ago by
doctor.dee005170
Bioinformatics Center, Pune
doctor.dee005170 wrote:

BLOSUM and PAM series matrices are available on NCBI ftp. See this link: ftp://ftp.ncbi.nih.gov/blast/matrices/

ADD COMMENTlink modified 17 hours ago • written 2 days ago by doctor.dee005170
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