Changes between Version 21 and Version 22 of PhyloWS_workgroup

Timestamp:

2008/02/12 14:48:33 (17 years ago)

Author:

czmasek

Comment:

--

PhyloWS_workgroup

@@ -16 +16 @@
  * The OTU (Operational Taxonomic Unit) perspective is an important use-case. 
   * Species tree hypothesis testing: splitting a given set of trees into subsets of trees as a function of compatibility to a given (set of) species tree(s). Degree of compatibility can be expressed as minimal sum of duplications needed to reconcile the gene with a species tree. I.e. measurement of the percentage of gene trees supporting an ecdysozoan versus a coelomata hypothesis.
+ * Problem: the query topology will be given with either gene name labels, or species name labels, but the labels of the trees will be OTUs.
+   * Hence, each OTU needs to be linked to the gene name(s) and taxon names, and it needs to be possible to specify that matching tree nodes use the linked taxon or gene names.
   * The analysis mentioned above could be extended by asking questions about the (majority of) functional categories supporting a given species tree. These examples require association of the following data with gene tree nodes: taxonomy identifier, gene identifier.
   * Gene tree analysis: similar to the Zmasek et al (2007) paper, one may want to build alignments and phylogenetic trees for all members of each protein  (family) of a biological network (e.g. apoptsis). After loading the trees into a database, one could then query the database for those gene trees that exhibit a given pattern (e.g. lineage specific gene expansion or gene loss).
-   * Problem: the query topology will be given with either gene name labels, or species name labels, but the labels of the trees will be OTUs.
-   * Hence, each OTU needs to be linked to the gene name(s) and taxon names, and it needs to be possible to specify that matching tree nodes use the linked taxon or gene names. 
   * In molecular and comparative genomics applications, one may want to find all trees that have been built for a certain sequence.
    * Problem: As above, querying by sequence will give the gene name or the sequence accession number to match by, but tree nodes will have OTUs as labels.