Homology Search By HMM-HMM Comparison Detects More Than Three Times As Many 
Remote Homologs as PSIBLAST or HMMER

Soeding, J; Lupas, AN

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Homology Search By HMM-HMM Comparison Detects More Than Three Times As Many Remote Homologs as PSIBLAST or HMMER

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Soeding, J
Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society;

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Lupas, AN
Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society;

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http://www.weizmann.ac.il/3dsig/2004/3dsigbook.pdf
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Citation

Soeding, J., & Lupas, A. (2004). Homology Search By HMM-HMM Comparison Detects More Than Three Times As Many Remote Homologs as PSIBLAST or HMMER. In 1st Structural Bioinformatics Meeting at ISMB/ECCB2004 (pp. 21-22).

Cite as: https://hdl.handle.net/21.11116/0000-0010-3E16-1

Abstract

We developed a homology search method based on pairwise comparison of profile HMMs. In an all-against-all benchmark (3691 SCOP 1.63 domains, < 20% sequence identity) the method detects 3-5 times more homologs than PSIBLAST or HMMER and between 25% and 100% more than profile-profile comparison tools COMPASS and PROF_SIM.