Changes between Version 25 and Version 26 of PhyloWS_workgroup

Timestamp:

2008/02/12 15:17:39 (17 years ago)

Author:

czmasek

Comment:

--

PhyloWS_workgroup

@@ -18 +18 @@
    * 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.
+  * 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, sequence identifier (which then, ideally, allows to retrieve functional data, such as GO).
   * 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).
   * In molecular and comparative genomics applications, one may want to find all trees that have been built for a certain sequence.