Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement |
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Authors: | Joel Hedlund Hans Jörnvall Bengt Persson |
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Institution: | 1.IFM Bioinformatics,Link?ping University,Link?ping,Sweden;2.Dept of Medical Biochemistry and Biophysics,Karolinska Institutet,Stockholm,Sweden;3.Dept of Cell and Molecular Biology,Karolinska Institutet,Stockholm,Sweden;4.National Supercomputer Centre (NSC) and Swedish E-science Research Centre (SERC),Link?ping University,Link?ping,Sweden |
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Abstract: | Background The Medium-chain Dehydrogenases/Reductases (MDR) form a protein superfamily whose size and complexity defeats traditional
means of subclassification; it currently has over 15000 members in the databases, the pairwise sequence identity is typically
around 25%, there are members from all kingdoms of life, the chain-lengths vary as does the oligomericity, and the members
are partaking in a multitude of biological processes. There are profile hidden Markov models (HMMs) available for detecting
MDR superfamily members, but none for determining which MDR family each protein belongs to. The current torrential influx
of new sequence data enables elucidation of more and more protein families, and at an increasingly fine granularity. However,
gathering good quality training data usually requires manual attention by experts and has therefore been the rate limiting
step for expanding the number of available models. |
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