A silly question .... What is the meaning of matrices like BLOSUM45, BLOSUM50, and so on ... They are listed on the following web site: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/ The literature calles them "alignment scoring matrices". I would like to understand the underlying logic and meaning. I understand they deal with sequences alignment. I would appreciate some suggestion about where to find a concised description of their usefulness, building rules, and usage. Thank you in advance, Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

Hi Maura, I don't think that this mailing list is the proper forum for this type of question. The first thing to do would be a simple google search of "alignment scoring matrix," and then, if that is not enough, maybe someone in your lab. Much to my supervisor's chagrin, I always come to him with very simple questions, and his answer is always the same: "google is your friend." tony On Fri, Jul 31, 2009 at 9:20 PM, <mauede@alice.it> wrote: > A silly question .... > What is the meaning of matrices like BLOSUM45, BLOSUM50, and so on ... > They are listed on the following web site: > http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/ > The literature calles them "alignment scoring matrices". > I would like to understand the underlying logic and meaning. I understand > they deal with sequences alignment. > > I would appreciate some suggestion about where to find a concised > description of their usefulness, building rules, > and usage. > > Thank you in advance, > Maura > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

On Sat, Aug 01, 2009 at 06:20:44AM +0200, mauede at alice.it wrote: > A silly question .... > What is the meaning of matrices like BLOSUM45, BLOSUM50, and so on ... You'll find plenty of information if you as you search engine of choice for "scoring matrix" and "sequence alignment". Once you got a rough ide I recommend Sean Eddys well written article: http://www.ncbi.nlm.nih.gov/pubmed/15286655 cu Philipp -- Dr. Philipp Pagel Lehrstuhl f?r Genomorientierte Bioinformatik Technische Universit?t M?nchen Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/