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percent?

I thought the way I learned it is that it was PERCENT Accepted Mutation, is that something else? --Frenkmelk 13:36, 28 August 2006 (UTC)[reply]

That is correct it is percent accepted mutation, if there are no objections will move the page in a week's time. And it is not 1 point mutation per 100 amino acids. it differs from protein to protein. for proteins like Histones the PAMs are much lower than other proteins.Kaushal mehta 15:11, 29 August 2006 (UTC)[reply]

I checked the paper of Dayhoff, Shwartz and Orcutt "A Model Evolutionary Change in Proteins" and at page 3, section "Mutation Probability Matrix for the Evolutionary Distance of One PAM" it is written “mutation probability matrix” Momet (talk) 10:32, 13 January 2008 (UTC)[reply]

Just to be clear, so no one thinks of moving it again, it's Point Accepted Mutations. But it sounds like it's said "percent" in some places so it's good to have the alternative phrasing right at the start.

But at least as Pevsner's textbook tells it, it's Point Accepted Mutations. Actually, they say it's Accepted Point Mutations but APM is harder to say tham PAM so they switched it.

--Qwerty0 (talk) 07:30, 26 October 2010 (UTC)[reply]

==

How can there be 250 point mutations per 100 residues? 128.39.241.235 (talk) 12:00, 10 February 2009 (UTC)[reply]

The PAM250 is calculated by taking PAM1, designed to change on average one residue, and applying it 250 times. After application of PAM250, most of the sites will suffer more than one mutation, and the result will probably be close to a random sequence. A few residues mutate very slowly, and those are the only ones with high weights at such large evolutionary distances.Whosasking (talk) 12:58, 10 February 2009 (UTC)[reply]

==

The wikipedia article about PAM-matrices claims that PAM-matrices imply a HMM-model. A reference to Pierre Baldi et. al [2] is included to that end. I found no relation in the article by Pierre Baldi et. al to PAM. The whole article does not mention PAM nor is the article by Dayhoff et. al cited in Pierre Baldi et. al. Please clarify the use of the reference. —Preceding unsigned comment added by 141.48.14.61 (talk) 15:14, 15 April 2010 (UTC)[reply]

Thank you for pointing this out. The PAM matrices imply a Markov model for the mutation process, not a hidden Markov model. I've replaced the references with two that are more on the topic.Whosasking (talk) 03:34, 16 April 2010 (UTC)[reply]