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ECCB
2008
IEEE

Connect the dots: exposing hidden protein family connections from the entire sequence tree

11 years 8 months ago
Connect the dots: exposing hidden protein family connections from the entire sequence tree
Motivation: Mapping of remote evolutionary links is a classic computational problem of much interest. Relating protein families allows for functional and structural inference on uncharacterized families. Since sequences have diverged beyond reliable alignment, these are too remote to identify by conventional methods. Approach: We present a method to systematically identify remote evolutionary relations between protein families, leveraging a novel evolutionary tree of all protein sequences and families. The tree is able to trace very faint links, owing to the robustness of considering the entire volume of pairwise sequence similarities at construction. Our method systematically scans the tree for clusters which partition exceptionally well into extant protein families, thus suggesting an evolutionary breakpoint in a putative ancient superfamily. Our method does not require family profiles (or HMMs), or multiple alignment. Results: Considering the entire Pfam database, we are able to su...
Yaniv Loewenstein, Michal Linial
Added 29 May 2010
Updated 29 May 2010
Type Conference
Year 2008
Where ECCB
Authors Yaniv Loewenstein, Michal Linial
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