Substitution matrix: Difference between revisions

Revision as of 05:29, 29 May 2025

Revision as of 08:47, 29 May 2025

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=== Newer matrices ===

A number of newer substitution matrices have been proposed to deal with inadequacies in earlier designs.

* JTT (19941992),. publishedPublished in the same year as BLOSOM, it also performs clustering and uses an implicit model. This may help reduce the systematic error from maximum parismony (MP), but also wastes sequence information.<ref name="WAG original paper"/>

* MDVTML (19922001), ana updatedPAM-like versionmatrix ofbased PAMon the alignments in the SYSTERS database, iteratively improved using a largermaximum likelihood estimator starting from the 1970s Dayhoff PAM datasetmodel.<ref name="pmid32954566">{{cite journal |last1=Trivedi |first1=R |last2=Nagarajaram |first2=HA |title=Substitution scoring matrices for proteins - An overview. |journal=Protein science : a publication of the Protein Society |date=November 2020 |volume=29 |issue=11 |pages=2150-2163 |doi=10.1002/pro.3954 |pmid=32954566 |pmc=7586916}}</ref>

* JTT (1994), published in the same year as BLOSOM, also performs clustering and uses an implicit model. This may help reduce the systematic error from maximum parismony (MP), but also wastes sequence information.<ref name="WAG original paper"/>

* VTML (2001), a PAM-like matrix based on the alignments in the SYSTERS database, iteratively improved using a maximum likelihood estimator starting from the 1970s Dayhoff PAM model.<ref name="pmid32954566"/>

* WAG (Wheelan And Goldman, 2001) uses a [[maximum likelihood]] estimating procedure instead of any form of MP over a "BRKALN" dataset. The substitution scores are calculated based on the likelihood of a change considering multiple tree topologies derived using [[neighbor-joining]]. The scores correspond to an [[substitution model]] which includes also amino-acid stationary frequencies and a scaling factor in the similarity scoring. There are two versions of the matrix: WAG matrix based on the assumption of the same amino-acid stationary frequencies across all the compared protein and WAG* matrix with different frequencies for each of included [[protein family|protein families]].<ref name="WAG original paper">{{cite journal |last1=Whelan |first1=Simon |last2=Goldman |first2=Nick |title=A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach |journal=Molecular Biology and Evolution |date=1 May 2001 |volume=18 |issue=5 |pages=691–699 |doi=10.1093/oxfordjournals.molbev.a003851 |pmid=11319253 |issn=0737-4038|doi-access=free }}</ref>

* LG (2008), which uses a larger dataset (Pfam-based) than WAG.<ref>{{cite journal |last1=Le |first1=S. Q. |last2=Gascuel |first2=O. |title=An Improved General Amino Acid Replacement Matrix |journal=Molecular Biology and Evolution |date=3 April 2008 |volume=25 |issue=7 |pages=1307–1320 |doi=10.1093/molbev/msn067}}</ref>