Amino Acid matrices freely downloadable url

Question

[RT!37]

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 !!

Answer 1

[pevsner]

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.

[RT!37]

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

[Dattatray Mongad]

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

[dukecomeback]

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

Answer 2

[Dattatray Mongad]

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