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Method Article
Matthew Berriman
Berriman Lab Group, Sanger Institute
Corresponding Author
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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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The authors declare no competing financial interests.
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An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Matthew Berriman
Berriman Lab Group, Sanger Institute
Corresponding Author
Version 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
The authors declare no competing financial interests.
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