Talk:BLOSUM

message: "The Henikoffs took a big database of trusted alignments (their BLOCKS database), and (in effect) only counted pairwise sequence alignments related by less than some threshold percentage identity. A threshold of 62% identity or less resulted in the target frequencies for the BLOSUM62 matrix. An 80% threshold gave the more highly conserved target frequencies of the BLOSUM80 matrix, and a 45% threshold gave the more divergent BLOSUM45 matrix."
Source:
Sean R. Eddy,
Where did the BLOSUM62 alignment score matrix come from?
Nature Biotechnology  22, 1035--1036 (2004)
doi:10.1038/nbt0804-1035
http://www.nature.com/nbt/journal/v22/n8/full/nbt0804-1035.html
"In order to avoid over-weighting closely-related sequences, the Henikoffs replaced groups
of proteins that have sequence identities higher than a threshold by either a single
representative or a weighted average. The threshold of 62% produces the commonly used
BLOSUM62 substitution matrix." 
Source:
Arthur M. Lesk,
Introduction to Bioinformatics
Oxford University Press, 2002, p.175
Winterschlaefer 15:52, 14 February 2007 (UTC)
replies: text: For what I know a BLOSUM62 matrix is good for alignements which have 62% or MORE identity XApple 00:32, 25 February 2007 (UTC)

text: It is definitely the case that the BLOSUM62 is based only on sequences that have 62% or more identity while the BLOSUM80 is based on sequences with 80% or more identity. Which one you use is up to your personal taste but as far as I know you would use a BLOSUM that is around your sequence identity where I agree with the speaker above. The error was fixed here. Greetings--hroest 03:39, 4 June 2008 (UTC)
thread_title:  BLOSUM62: more or less than 62% identity? 

message: This badly needs a picture of a typical Blosum matrix XApple 14:52, 12 February 2007 (UTC)
replies: text: It did get one. --hroest 05:50, 7 March 2008 (UTC)
thread_title:  Illustration 

message: Some smart people say that one must say "BLOSUM" instead of "BLOSUM matrix" because the "M" in BLOSUM already means "matrix". The latter is correct, but the term BLOSUM is by now a name, not just an abbreviation. BLOSUM is a technical term. It is common sense in the scientific community to speak of "BLOSUM matrices". Just saying "BLOSUM" is counterintuitive and not colloquial.
Furthermore, if we wanted to get it linguistically really right, the article itself contained mistakes. It wrote: "To calculate a matrix for BLOSUM, ...". This is grammatically wrong, whatever opinion one has about BLOSUM matrices. 134.76.81.25 (talk) 10:49, 22 September 2010 (UTC)
thread_title:  "BLOSUM matrix" is correct 

message: Hello fellow Wikipedians,
I have just modified one external link on BLOSUM. Please take a moment to review my edit. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit this simple FaQ for additional information. I made the following changes:
*Added archive https://web.archive.org/web/20130309015755/http://birec.org/sandbox/omamasaudtutorial to http://www.birec.org/sandbox/omamasaudtutorial
When you have finished reviewing my changes, you may follow the instructions on the template below to fix any issues with the URLs.
Cheers.—InternetArchiveBot (Report bug) 09:31, 14 September 2017 (UTC)
thread_title:  External links modified