Status of compilation of assemblies for deep green (Norm):
First 40 data sets are currently being run through Mike Barker's DupPipe and TransPipe at Arizona, running at a rate of 3-4 taxa/day.
Michael Gonzales has installed Hamstr on TACC cluster(s). Mike will test installation, and Norm will start using Hamstr to sort uniscripts next week.
Ks Plots and transpipe - Now running on Mike B's cluster at Arizona.
TACC repository for OneKp data needs to be synced with WestGrid repository (Mike G. and Chris J.)
BLAST portal (Mike G.) - Next on Mike's priority list (after testing Hamstr and updating TACC data repository). Raj can help.
Portal for searching terms of best BLAST hits (Mike G.) - Mike has a database of BLASTX results including (Query = 1kp assembly sequence, Hit = sequence from 25 genome database):
Query_name
Query_sequence
Query_accession
Query_description
Query_number_of_hits
Hit_name
Hit_accession
Hit_description
Hit_significance (e-value)
Hit_num_hsp (number of hsp)
Alignments not included - too bad but simply reporting hits with Query sequence would be useful for OneKp consortium.
Installation of SATe on TACC cluster(s) (Mike G.) - Mike talking with Tandy Warnow.
Brief demo of Tree ReconciliationViewer (Jim and Naim)
Folks were impressed with Naim's demo. Questions discussed including:
Font size and node symbols too small.
Nodal support values for trees - Database can accommodate support values.
How will tree reconciliations be done for OneKp data:
Notung would use estimated gene trees and species tree
TreeBEST and PrIME-GSR would assume the estimated species tree is correct and re-estimated gene trees with reconciliations using penalized likelihood and a Bayesian approach, respectively.
Accuracy of reconciliations - Jamie Estill is comparing TreeBEST reconciliations with six-taxon synteny-based reconciliation constructed by John Bowers.
Action Items:
Norm - Run Hamstr on translations coming from Mike B's TransPipe; Assess differences between SOAP and CLC+ assemblies for exemplar taxa; work with Jim and Raj to complete compilation cDNA data sets for all taxa in "deep green" study.
MIke G. - Complete installation of Hamstr ; Sync TACC OneKP data repository with Westgrid repository; Finalize OneKp blast portal (Jim and Raj could help could help simplify blast database - e.g. split into smaller taxon databases, remove all database sequences shorter than some threshold (???)); Develop front end for blast results database (Raj could help).