PhyloFacts

[…] m [], SMART [], PRINTS [], InterPro [], CDD [], CATH [], SCOP [] and ECOD []) generally considered to be evolutionary independent modules having distinct functional properties []. Some resources like PhyloFacts [] also provide classification of both full-length proteins and domains. At least two thirds of eukaryotic and more than a half of prokaryotic proteins are composed of multiple domains [] a […]

[…] Orthology analysis was performed using the PHOG web server (http://phylofacts.berkeley.edu/orthologs/) (Datta et al., ). The sequences of conserved domains with similarity over 70% and an “E” value of 0.0 were selected as queries. The selected sequences of conserved […]

[…] ere defined by r2 > 0.8. Genes with non-synonymous SNPs that assort with soil type (allele frequency difference > 0.7) had Mt3.5.1 annotations confirmed using the structural phylogenomic encyclopedia PhyloFacts [] and the orthology group prediction tool PHOG []. Protein alignments containing sequences from numerous angiosperms were used to identify conserved amino acid positions. For selected cand […]

[…] t if they are present in at least 5% of the input sequences and have a p-value below the threshold of 1e−10. Matches to known motifs were discovered from the Jaspar v4 database (vertebrate CORE, FAM, PHYLOFACTS, POLII, CNE and SPLICE) () and only significant motifs (Q-value ≤ 0.05) were reported. In total, there were 1664 de-novo motifs and of these, 1152 had a significant match to Jaspar motifs. […]

[…] be limited to Pfam, which uses HMMs to model protein domains (). Recent years have seen the generation of databases of HMMs of full-length and phylogenetically diverse protein families. This includes Phylofacts () and the SiftingFamilies database (), which, like EggNOG, tend to be frequently updated.Protein family classification of metagenomic reads tends to require substantial computing resources […]

[…] Orthology analysis was performed using the PHOG web server (http://phylofacts.berkeley.edu/orthologs/) . The sequences that have similarity over 70% and an “E” value of 0.0 were selected. The selected sequences were used in a BLASTP search against the V. vinifera pro […]