Predicting functional sites with an automated algorithm suitable for heterogeneous datasets

David, Lawrence A.; Livesay, Dennis R.

doi:10.1186/1471-2105-6-116

Cited by 25 publications

(8 citation statements)

References 41 publications

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“…We subjected sequences from each clade to motif analysis using MINER v2.0 [16-18]. Clades II and IV were excluded from the analysis due to their small sizes.…”

Section: Resultsmentioning

confidence: 99%

“…The large number of BAHD genes available from sequenced plant genomes presents an opportunity to expand the analysis of conserved motifs in this family beyond the two known functional domains, HXXXD and DFGWG. We subjected sequences from each clade to motif analysis using MINER v2.0 [ 16 - 18 ]. Clades II and IV were excluded from the analysis due to their small sizes.…”

Section: Resultsmentioning

confidence: 99%

“…Aligned protein sequences from MAFFT were split into separate FASTA files by clade using BioEdit, and subjected to motif analysis using the MINER v2.0 web interface with default settings [ 16 - 18 ]. Because a minimum of 25 sequences is recommended by the program to achieve good statistical support, Clade IV (five members) and Clade II (18 members) were excluded from the analysis.…”

Section: Methodsmentioning

confidence: 99%

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Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues

2011

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BackgroundBAHD acyltransferases are involved in the synthesis and elaboration of a wide variety of secondary metabolites. Previous research has shown that characterized proteins from this family fall broadly into five major clades and contain two conserved protein motifs. Here, we aimed to expand the understanding of BAHD acyltransferase diversity in plants through genome-wide analysis across five angiosperm taxa. We focus particularly on Populus, a woody perennial known to produce an abundance of secondary metabolites.ResultsPhylogenetic analysis of putative BAHD acyltransferase sequences from Arabidopsis, Medicago, Oryza, Populus, and Vitis, along with previously characterized proteins, supported a refined grouping of eight major clades for this family. Taxon-specific clustering of many BAHD family members appears pervasive in angiosperms. We identified two new multi-clade motifs and numerous clade-specific motifs, several of which have been implicated in BAHD function by previous structural and mutagenesis research. Gene duplication and expression data for Populus-dominated subclades revealed that several paralogous BAHD members in this genus might have already undergone functional divergence.ConclusionsDifferential, taxon-specific BAHD family expansion via gene duplication could be an evolutionary process contributing to metabolic diversity across plant taxa. Gene expression divergence among some Populus paralogues highlights possible distinctions between their biochemical and physiological functions. The newly discovered motifs, especially the clade-specific motifs, should facilitate future functional study of substrate and donor specificity among BAHD enzymes.

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“…We subjected sequences from each clade to motif analysis using MINER v2.0 [16-18]. Clades II and IV were excluded from the analysis due to their small sizes.…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues

2011

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“…Many features of nucleic acids can be used in bioinformatic algorithms as motifs for description of their genomic variability and their better understanding. Individual sequence motifs are recognized by their order and nucleotide preference, and many motif discovery algorithms have been used in different molecular or bioinformatic studies [31][32][33][34].…”

Section: Technical Approaches and Methodsologies For Pcr Screening Ofmentioning

confidence: 99%

Application of Genomic Data for PCR Screening of Bet v 1 Conserved Sequence in Clinically Relevant Plant Species

Žiarovská¹,

Zeleňáková²

2019

Systems Biology

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Bet v 1 is a highly immunogenic protein, which is the main cause of sensitivity to birch pollen and is described as the main birch allergen. Despite the structural similarity, Bet v 1 homologs show different properties and immunoreactivity. Here, the bioinformatic algorithms were applied for known Bet v 1 homologous nucleic acids sequences to find homology and conserved regions. Genomic sequences of PR proteins of two different fruit species, which allergens belong to PR proteins of the same type as Bet v 1, were selected to design degenerate primers. Subsequently, screening of the presence of Bet v 1 conserved genomic sequence was performed in 45 clinically relevant plant species.

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“…The sequence based prediction methods used sequence homology information or/and conserved family patterns/motifs [ 3 – 5 ], sensitive sequence-based scoring functions, amino acid stereochemical features [ 6 , 7 ], conservation scores such as Von Neumann entropy, relative entropy, Jensen-Shannon divergence and sum-of-pairs measure [ 3 , 8 ] to predict catalytic residues. Other prediction methods used phylogenetic motifs and phylogenetic trees [ 9 , 10 ]. CRpred is one of the best sequence based methods that uses various sequence features such as residue type, hydrophobicity, and PSI-BLAST profiles [ 11 ] in a Support Vector Machine (SVM) based binary classification of residues into catalytic and non-catalytic residues.…”

Section: Introductionmentioning

confidence: 99%

CSmetaPred: a consensus method for prediction of catalytic residues

et al. 2017

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BackgroundKnowledge of catalytic residues can play an essential role in elucidating mechanistic details of an enzyme. However, experimental identification of catalytic residues is a tedious and time-consuming task, which can be expedited by computational predictions. Despite significant development in active-site prediction methods, one of the remaining issues is ranked positions of putative catalytic residues among all ranked residues. In order to improve ranking of catalytic residues and their prediction accuracy, we have developed a meta-approach based method CSmetaPred. In this approach, residues are ranked based on the mean of normalized residue scores derived from four well-known catalytic residue predictors. The mean residue score of CSmetaPred is combined with predicted pocket information to improve prediction performance in meta-predictor, CSmetaPred_poc.ResultsBoth meta-predictors are evaluated on two comprehensive benchmark datasets and three legacy datasets using Receiver Operating Characteristic (ROC) and Precision Recall (PR) curves. The visual and quantitative analysis of ROC and PR curves shows that meta-predictors outperform their constituent methods and CSmetaPred_poc is the best of evaluated methods. For instance, on CSAMAC dataset CSmetaPred_poc (CSmetaPred) achieves highest Mean Average Specificity (MAS), a scalar measure for ROC curve, of 0.97 (0.96). Importantly, median predicted rank of catalytic residues is the lowest (best) for CSmetaPred_poc. Considering residues ranked ≤20 classified as true positive in binary classification, CSmetaPred_poc achieves prediction accuracy of 0.94 on CSAMAC dataset. Moreover, on the same dataset CSmetaPred_poc predicts all catalytic residues within top 20 ranks for ~73% of enzymes. Furthermore, benchmarking of prediction on comparative modelled structures showed that models result in better prediction than only sequence based predictions. These analyses suggest that CSmetaPred_poc is able to rank putative catalytic residues at lower (better) ranked positions, which can facilitate and expedite their experimental characterization.ConclusionsThe benchmarking studies showed that employing meta-approach in combining residue-level scores derived from well-known catalytic residue predictors can improve prediction accuracy as well as provide improved ranked positions of known catalytic residues. Hence, such predictions can assist experimentalist to prioritize residues for mutational studies in their efforts to characterize catalytic residues. Both meta-predictors are available as webserver at: http://14.139.227.206/csmetapred/.Electronic supplementary materialThe online version of this article (10.1186/s12859-017-1987-z) contains supplementary material, which is available to authorized users.

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Predicting functional sites with an automated algorithm suitable for heterogeneous datasets

Cited by 25 publications

References 41 publications

Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues

Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues

Application of Genomic Data for PCR Screening of Bet v 1 Conserved Sequence in Clinically Relevant Plant Species

CSmetaPred: a consensus method for prediction of catalytic residues

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