From zhu@iastate.edu Thu Jan 10 15:47:50 2008 Date: Thu, 10 Jan 2008 15:47:28 -0600 From: Zhiliang Hu To: Multiple Recipients of Subject: What's new on the NAGRP animal genome web site (#1, 2008) What's new on the NAGRP animal genome web site: - 1 - A new linux cluster computer with 8 nodes, a total of 16 processors is commissioned. We have installed the mpiblast, and developed web tools to accept, queue blast jobs and send results to users. This is a great boost to the blast capacity we have. URL: http://www.animalgenome.org/blast/mpiblast.html To make better use of its computing power for the community, we need inputs from you on, (1) what sequence database we should build (besides the genomes of human, cattle and chicken)? (2) Any other applications to utilize its parallel computing power? Discussions on large scale data analysis may also be useful. - 2 - The Animal QTLdb Release #6 -- A new release of Animal QTLdb is available. Several things are new in this release: (1) the number of curated QTL for cattle, chicken and pigs are 1,124, 657, and 1,675 respectively; (2) More structural genomic information is aligned with respective QTL maps, which include alignments of 18,183 SNPs, 14,728 affy-microarray elements, 15,627 oligo-microarray elements to the bovine genome, 4,528 new microsatellites, 435 gene-based SNPs, 18,487 affy-microarray elements, 16,700 oligo- microarray elements to swine genome, and 2,978 SNPs to chicken genome. URL: http://www.animalgenome.org/QTLdb/ - 3 - Additional 838 porcine microsatellites with repeat motives of three to six bases have been added to the Pig QTLdb for alignment. This is an addition to the previously aligned 4,528 porcine microsatellite markers. Thanks to Peter Karlskov-Mortensen and Merete Fredholm from the Royal Veterinary and Agricultural Univ. of Denmark for providing the data. URL: http://www.animalgenome.org/QTLdb/tmp/03219.html - 4 - Animal Trait Ontology Project web site was renovated, with additions of (1) a user guideline for collaborators, (2) a discussion forum for the project participants, (3) AmiGO browser to view the ATO hierarchy. Thanks to Laron Hughes for some of the works he put in on this. URL: http://www.animalgenome.org/bioinfo/projects/ATO/ - 5 - 1.8 million cattle SNPs from Baylor are aligned to cattle QTL maps. Thanks to George Weinstock of the Texas Medical Center for his kind helps to obtain the new cattle SNP data. URL: http://www.animalgenome.org/QTLdb/cattle.html - 6 - A preliminary experiment to align and display microarray expression data seems successful. Thanks to Shu-hong Zhao from Huazhong University for providing the testing data. URL: http://www.animalgenome.org/QTLdb/pig.html Check out "what's new" page for more up-to-date information on the site: http://www.animalgenome.org/news/whatsnew.html -- NAGRP Bioinfo Team bioinfo-team@animalgenome.org