All entries for September 2008
September 26, 2008
The JGI are now calling for community EST’s (and other sequence, linkage, mapping related to H97) to support the forthcoming annotation effort.
JGI will be interested in any resources the community has to offer to aid in the annotation, e.g. ESTs, BAC libraries, physical and genetic maps.
http://snipurl.com/3uxgu-mpc [JGI Genomes]
*JGI News Update (Thu, 18 Sep 2008)*
The A. bisporus cDNA libs are in the 454 sequencing queue and JGI should have sequence within a couple weeks
The JGI can include external ESTs with their ESTs for clustering.
JGI need ESTs (not assembled consensus sequences) in fasta format with qual scores if available.
They would prefer that ESTs are vector and adaptor trimmed (and qual trimmed if no qual file is available).
The JGI will screen out rRNA and prokaryotic seqs (for Euk projects) and separate out organelle ESTs if available for this specific genus species.
If there are EST pairing information patterns in the read names they would like to know.
If you have any Agaricus bisporus data you might like to contribute to the project, please contact me at your earliest convenience
*PLEASE NOTE – all data will enter the public domain, the JGI will not separate ‘private ESTs’ *
September 05, 2008
The three Agaricus bisporus var. bisporus H97 sequencing libraries (3kb, 6-8kb & fosmids) have recently passed QC. H97 will now be scheduled for the ~4X checkpoint sequencing & assembly. The estimated time frame for the availability of the assembly from the 4X dataset is between Jan-Mar 2009.
Additionally, titration runs on three 454 EST libraries for Agaricus bisporus U1 are completed. All three samples passed QC and JGI will proceed with bulk runs.