Question: Amino Acid matrices freely downloadable url
0
gravatar for RT!37
14 months 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 • 521 views
ADD COMMENTlink modified 14 months ago by pevsner420 • written 14 months ago by RT!370
5
gravatar for pevsner
14 months 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 14 months ago by pevsner420

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

ADD REPLYlink written 14 months 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 14 months ago by Dattatray Mongad340

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 10 months ago by dukecomeback40
3
gravatar for Dattatray Mongad
14 months ago by
National Centre for Cell Science, Pune
Dattatray Mongad340 wrote:

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

ADD COMMENTlink modified 14 months ago • written 14 months ago by Dattatray Mongad340
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