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October 13, 2008

EST data sets sent to JGI

Agaricus bisporus Genome Sequencing - Project updates

[29 Sept 2008] 

Warwick sequence database (ca 1700 seqs) sent to the JGI, these comprise

1-813 EMBL nucleotide database sequences related to Agaricus bisporus

814-1066 miscellaneous cDNA library sequences

1067-1513 SSH differential expression during mushroom development (vegetative mycelium to initials)

1517-1592 SSH infection (fungal pathogen) response genes

1592-1773 SSH infection (viral) response genes

[13 Oct 2008] 

Many thanks to Dr. Jurriaan J. Mes (Agrotechnology and Food Sciences, Group Wageningen UR) who has kindly provided an additional data set of ca 1200 SSH sequences

PLEASE NOTE - There is still time to include additional data sets - interested parties with suitable data should contact me at their earliest convenience

September 26, 2008

Agaricus bisporus Genome Sequence – JGI Calling for Community EST Data

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.

jgi_logo [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’ *

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