Question: Amino Acid matrices freely downloadable url
0
gravatar for RT!37
2.1 years ago by
RT!3720
India
RT!3720 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 • 1.1k views
ADD COMMENTlink modified 2.1 years ago by pevsner420 • written 2.1 years ago by RT!3720
5
gravatar for pevsner
2.1 years 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 2.1 years ago by pevsner420

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

ADD REPLYlink written 2.1 years ago by RT!3720
1

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

ADD REPLYlink written 2.1 years ago by Dattatray Mongad350

Hi, I'm quiet new to evolution, do you know why there is so many version of Jones matrices there? Thank you very much.

ADD REPLYlink written 22 months ago by dukecomeback40
3
gravatar for Dattatray Mongad
2.1 years ago by
National Centre for Cell Science, Pune
Dattatray Mongad350 wrote:

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

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Dattatray Mongad350
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