Homology was detected to 45% of Arabidopsis, 39% of Populus, and 22% of Oryza gene models (E value 10-5).
Finally, we utilized the Gene Ontology (GO) classifications from the Arabidopsis best-hit gene models (E value 10-5).
We estimated Ka/Ks for 2,001 E. grandis contigs that have at least three high confidence SNPs and one positive BlastX hit against Arabidopsis gene models (E value 10-5) [see Additional file 1].
To identify expressed genes that were not predicted in the original genome annotation [ 2], we searched among the set of 4,487 FLcDNAs with a stringent BLAT match to the genome that did not match to any of the 45,555 predicted gene models (E value ≥ 1e-50).
The statistical significance threshold for including a sequence in the model (E-value) used by PSI-BLAST in the next iteration was either 10-2 or 10-3, BLOSUM45 was used as a substitution matrix.
The input data for a Blastn run are: query sequence, sequence set to be searched, Expected number of chance matches in a random model (E-value), maximum number of hits to be displayed, maximum number of aligned sequences to be displayed, size of the string to be searched in pairwise comparison (word size), scoring parameters, and filtering and masking options.
Ancillary synteny data for each unigene was added, including the best hit for the unigene from pre-computed BLASTN analysis against Brachypodium, rice and sorghum gene models (E-value cut-off 1E-50), together with a measure of transcript abundance, expressed as reads per kilobase per million mapped reads (RPKM values).
For each of the three A. millepora GiMAP-like predicted proteins, the NTPase domain matches best the AIG1 model pfam04548 (e value < E-12 in each case; Cluster012256 (GiMAP1) = 9.57E-14; Cluster 024980 (GiMAP2) = 1.53E-19; Cluster015015 (GiMAP3) = 5.58E-13), whereas the significance values for matches to other related domains (e.g. Toc-34, Ras, Septin) were much lower (Additional file 4).
Out of 3,898 DETs, 2,968 (76.14%) were matched with Arabidopsis gene models with E value ≤ e-10 (Additional file 1).
When tested against the Kinomer HMMs [ 44], the two P. infestans proteins best-matched the TK model with E values of 10-15 and 10-45, respectively.
Among 118,013 unigenes longer than 100 bp 38% have similarity to at least one gene model at an E value of 10-5, 28% at an E value of 10-10, and 15% at an E value of 10-20.
