Changes between Version 1 and Version 2 of WikiStart


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Timestamp:
Mar 14, 2011, 2:32:19 PM (9 years ago)
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victor.de.jager@…
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  • WikiStart

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    11
    22= Welcome to project loft =
     3René TJM van der Heijden, Berend Snel, Vera van Noort and Martijn A Huynen[[BR]]
     4Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
     5
     6'''Abstract'''
     7Background: Orthology is one of the cornerstones of gene function prediction. Dividing the
     8phylogenetic relations between genes into either orthologs or paralogs is however an
     9oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature
     10of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two
     11species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit
     12them. Published procedures to extract orthologous groups from phylogenetic trees do not allow
     13identification of orthology at various levels of resolution, nor do they document the relations
     14between the orthologous groups.
     15
     16'''Results:''' We introduce "levels of orthology" to describe the multi-level nature of gene relations. This
     17is implemented in a program LOFT (Levels of Orthology From Trees) that assigns hierarchical
     18orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene
     19duplication events in a tree LOFT can be instructed either to perform classical species-tree
     20reconciliation or to use the species overlap between partitions in the tree. The hierarchical
     21orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between
     22genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual
     23inspection of (large) trees. A benchmark for orthology prediction, that takes into account the
     24varying levels of orthology between genes, shows that the phylogeny-based high-resolution
     25orthology assignments made by LOFT are reliable.
     26
     27'''Conclusion:''' The "levels of orthology" concept offers high resolution, reliable orthology, while
     28preserving the relations between orthologous groups. A Windows as well as a preliminary Java
     29version of LOFT is available from svn co https://trac.nbic.nl/svn/loft loft or http://www.cmbi.ru.nl/LOFT
     30
     31The original publication is [http://www.biomedcentral.com/1471-2105/8/83 available]
     32
    333
    434== Mailing lists ==