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PhyloFacts specifications

Information


Unique identifier OMICS_05358
Name PhyloFacts
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Kimmen Sjölander

Publications for PhyloFacts

PhyloFacts citations

 (14)
library_books

Diversity in protein domain superfamilies

2015
PMCID: 4686048
PMID: 26451979
DOI: 10.1016/j.gde.2015.09.005

[…] 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 […]

library_books

Mitogen activated protein kinase cascades in Vitis vinifera

2015
Front Plant Sci
PMCID: 4511077
PMID: 26257761
DOI: 10.3389/fpls.2015.00556

[…] 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 […]

library_books

The ecological genomic basis of salinity adaptation in Tunisian Medicago truncatula

2014
BMC Genomics
PMCID: 4410866
PMID: 25534372
DOI: 10.1186/1471-2164-15-1160

[…] 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 […]

library_books

Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells

2014
Nucleic Acids Res
PMCID: 4267662
PMID: 25428352
DOI: 10.1093/nar/gku1254

[…] 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. […]

library_books

An introduction to the analysis of shotgun metagenomic data

2014
Front Plant Sci
PMCID: 4059276
PMID: 24982662
DOI: 10.3389/fpls.2014.00209

[…] 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 […]

library_books

Whole Genome Survey of the Putative ATP Binding Cassette Transporter Family Genes in Vitis vinifera

2013
PLoS One
PMCID: 3823996
PMID: 24244377
DOI: 10.1371/journal.pone.0078860

[…] 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 […]

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PhyloFacts institution(s)
Department of Bioengineering, University of California, Berkeley, CA, USA
PhyloFacts funding source(s)
Supported by a Presidential Early Career Award for Scientists and Engineers (PECASE) from the National Science Foundation, and by an R01 from the National Human Genome Research Institute of the NIH.

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