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Method Article
Identification of lineage-specific gene family expansions in a database of gene families
Matthew Berriman
Berriman Lab Group, Sanger Institute
Corresponding Author
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This work is licensed under a CC BY 4.0 License. Read Full License
Gene families specific to, or with significantly changed membership in, particular lineages compared to outgroups may reflect important lineage-specific changes in biology. Here we describe a computational protocol to identify gene families that vary greatly in gene count across a species tree. This protocol uses three different metrics to capture aspects of this variability, and calculates them for each family in an in-house database of gene families (e.g. built using the Ensembl Compara pipeline). One metric (Cv) identifies families that vary a lot in gene count across the species tree, and the other two (Emax, Zmax) identify families that have an elevated gene count in a certain clade of the species tree. Our protocol controls for differences in gene counts due to fragmented assemblies.
Keywords
Gene families, gene family expansions, Compara, lineage-specific expansions, Ensembl
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This is a preprint. It has not completed peer review.
Method Article
Identification of lineage-specific gene family expansions in a database of gene families
Matthew Berriman
Berriman Lab Group, Sanger Institute
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 14 May, 2018
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Gene families specific to, or with significantly changed membership in, particular lineages compared to outgroups may reflect important lineage-specific changes in biology. Here we describe a computational protocol to identify gene families that vary greatly in gene count across a species tree. This protocol uses three different metrics to capture aspects of this variability, and calculates them for each family in an in-house database of gene families (e.g. built using the Ensembl Compara pipeline). One metric (Cv) identifies families that vary a lot in gene count across the species tree, and the other two (Emax, Zmax) identify families that have an elevated gene count in a certain clade of the species tree. Our protocol controls for differences in gene counts due to fragmented assemblies.
Figure 1
Figure 2
Figure 3