Comparative Genomics of Plant Species

Homology searches were performed against public sequence databases. The newest versions as of February 2010 of the protein sequences of Arabidopsis (TAIR 9), Vitis (Sept 2009 build) and Populus (version 2.0, Phytozome) were used to construct the individual BLAST datasets. The Eucalyptus public dataset (EucAll) consisted of 45,442 entries in Genbank (downloaded March 2010), 13,930 entries from the Eucalyptus Wood unigenes and ESTs [33 (link)], E. grandis leaf tissue ESTs (120,661 entries from DOE-JGI-produced 454 sequences, http://eucalyptusdb.bi.up.ac.za/) and 190,106 Unigenes and singlets from E. grandis 454 data [15 (link)]. The BLAST e-value threshold was set at 1e^-10, with a minimum alignment length of 100 nucleotides (33 amino acids). Functional annotation (GO and KEGG) was performed using BLAST2GO [54 (link)], using the default annotation parameters (BLAST e-value threshold of 1e^-06, Gene Ontology annotation threshold of 55). InterPro annotations were performed using InterProScan (http://www.ebi.ac.uk/Tools/InterProScan/).

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Mizrachi E., Hefer C.A., Ranik M., Joubert F, & Myburg A.A. (2010). De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq. BMC Genomics, 11, 681.

Publication 2010

Amino acids Arabidopsis Ests Eucalyptus Leaf Nucleotides Populus Protein sequences Tissue Vitis

Corresponding Organization :

Other organizations : University of Pretoria

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Variable analysis

independent variables

Homology searches were performed against public sequence databases

dependent variables

Functional annotation (GO and KEGG) was performed using BLAST2GO
InterPro annotations were performed using InterProScan

control variables

The BLAST e-value threshold was set at 1e-10, with a minimum alignment length of 100 nucleotides (33 amino acids)
BLAST2GO used a default annotation parameters (BLAST e-value threshold of 1e-06, Gene Ontology annotation threshold of 55)

Annotations

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