Berkeley PHOG: PhyloFacts orthology group prediction web server

Datta, Ruchira S.; Meacham, Christopher A.; Samad, Bushra; Neyer, Christoph; Sjölander, Kimmen

doi:10.1093/nar/gkp373

Cited by 65 publications

(60 citation statements)

References 24 publications

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“…Further, we used PHOG (http://phylofacts.berkeley.edu/orthologs/) to predict super-orthologs based on phylogenetic analysis [28]. Finally, we used Phyre (http://www.sbg.bio.ic.ac.uk/~phyre/) to predict three dimensional structure using homology modeling, which does not rely on conservation of protein sequence [29].…”

Section: Resultsmentioning

confidence: 99%

A Novel Human Cytomegalovirus Locus Modulates Cell Type-Specific Outcomes of Infection

et al. 2011

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Clinical strains of HCMV encode 20 putative ORFs within a region of the genome termed ULb′ that are postulated to encode functions related to persistence or immune evasion. We have previously identified ULb′-encoded pUL138 as necessary, but not sufficient, for HCMV latency in CD34+ hematopoietic progenitor cells (HPCs) infected in vitro. pUL138 is encoded on polycistronic transcripts that also encode 3 additional proteins, pUL133, pUL135, and pUL136, collectively comprising the UL133-UL138 locus. This work represents the first characterization of these proteins and identifies a role for this locus in infection. Similar to pUL138, pUL133, pUL135, and pUL136 are integral membrane proteins that partially co-localized with pUL138 in the Golgi during productive infection in fibroblasts. As expected of ULb′ sequences, the UL133-UL138 locus was dispensable for replication in cultured fibroblasts. In CD34+ HPCs, this locus suppressed viral replication in HPCs, an activity attributable to both pUL133 and pUL138. Strikingly, the UL133-UL138 locus was required for efficient replication in endothelial cells. The association of this locus with three context-dependent phenotypes suggests an exciting role for the UL133-UL138 locus in modulating the outcome of viral infection in different contexts of infection. Differential profiles of protein expression from the UL133-UL138 locus correlated with the cell-type dependent phenotypes associated with this locus. We extended our in vitro findings to analyze viral replication and dissemination in a NOD-scid IL2Rγc null-humanized mouse model. The UL133-UL138 NULL virus exhibited an increased capacity for replication and/or dissemination following stem cell mobilization relative to the wild-type virus, suggesting an important role in viral persistence and spread in the host. As pUL133, pUL135, pUL136, and pUL138 are conserved in virus strains infecting higher order primates, but not lower order mammals, the functions encoded likely represent host-specific viral adaptations.

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Section: Resultsmentioning

confidence: 99%

A Novel Human Cytomegalovirus Locus Modulates Cell Type-Specific Outcomes of Infection

et al. 2011

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“…''Phylogenomics'' (Eisen 1998) is the use of phylogenetics to systematically reconstruct the ancestry of thousands of gene families across many related genomes, and in recent years it has been pursued in a variety of ways (Zmasek and Eddy 2002;Li et al 2006;Huerta-Cepas et al 2007;Wapinski et al 2007;Butler et al 2009;Datta et al 2009;Vilella et al 2009;Mi et al 2010).…”

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confidence: 99%

Unified modeling of gene duplication, loss, and coalescence using a locus tree

2012

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Gene phylogenies provide a rich source of information about the way evolution shapes genomes, populations, and phenotypes. In addition to substitutions, evolutionary events such as gene duplication and loss (as well as horizontal transfer) play a major role in gene evolution, and many phylogenetic models have been developed in order to reconstruct and study these events. However, these models typically make the simplifying assumption that population-related effects such as incomplete lineage sorting (ILS) are negligible. While this assumption may have been reasonable in some settings, it has become increasingly problematic as increased genome sequencing has led to denser phylogenies, where effects such as ILS are more prominent. To address this challenge, we present a new probabilistic model, DLCoal, that defines gene duplication and loss in a population setting, such that coalescence and ILS can be directly addressed. Interestingly, this model implies that in addition to the usual gene tree and species tree, there exists a third tree, the locus tree, which will likely have many applications. Using this model, we develop the first general reconciliation method that accurately infers gene duplications and losses in the presence of ILS, and we show its improved inference of orthologs, paralogs, duplications, and losses for a variety of clades, including flies, fungi, and primates. Also, our simulations show that gene duplications increase the frequency of ILS, further illustrating the importance of a joint model. Going forward, we believe that this unified model can offer insights to questions in both phylogenetics and population genetics.

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“…A Database containing the predictions of different ortholog detection methods is created. Protein sequence ortholog predictions were obtained from the Inparanoid database, OMA, PHOG [33] and FATCAT [34] web servers. For integrating the data from different ortholog detection databases the main problem encountered is the use of different gene identifiers by different ortholog detection databases.…”

Section: A Collection Of Input Datamentioning

confidence: 99%

Phylogenetic Method for High-Throughput Ortholog Detection

Gupta¹,

Singh²

2015

IJIEEB

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Abstract-Accurate detection of orthologous proteins is a key aspect of comparative genomics. Orthologs in different species can be used to predict the function of uncontrived genes from model organisms as they retain the same biological function through the path of evolution. Orthologs can be inferred using phylogenetic, pair-wise similarity or synteny based methods. The study here describes a computational method for detecting orthologs of a protein. A phylogenetic tree based approach is used for identification of orthologous proteins. A Combination of species overlap algorithm and patristic distances is used for detecting orthologs of a protein from a set of FASTA sequences. Patristic distances have been used to drill the orthology predictions of any protein down to its closest orthologs. The approach gives a considerably good accuracy and has high specificity and precision. The use of Distance threshold allows controlling the stringency level of predictions so that the closeness and proximity between the protein of interest and its orthologs can be adjusted.

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Berkeley PHOG: PhyloFacts orthology group prediction web server

Cited by 65 publications

References 24 publications

A Novel Human Cytomegalovirus Locus Modulates Cell Type-Specific Outcomes of Infection

A Novel Human Cytomegalovirus Locus Modulates Cell Type-Specific Outcomes of Infection

Unified modeling of gene duplication, loss, and coalescence using a locus tree

Phylogenetic Method for High-Throughput Ortholog Detection

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