Cargando…

BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins

BACKGROUND: Automated function prediction has played a central role in determining the biological functions of bacterial proteins. Typically, protein function annotation relies on homology, and function is inferred from other proteins with similar sequences. This approach has become popular in bacte...

Descripción completa

Detalles Bibliográficos
Autores principales:	Kankainen, Matti, Ojala, Teija, Holm, Liisa
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2012
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386020/ https://www.ncbi.nlm.nih.gov/pubmed/22335941 http://dx.doi.org/10.1186/1471-2105-13-33

Ejemplares similares

Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis
por: Ojala, Teija, et al.
Publicado: (2014)

POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets
por: Kankainen, Matti, et al.
Publicado: (2005)

Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana
por: Kankainen, Matti, et al.
Publicado: (2006)

Adhesive polypeptides of Staphylococcus aureus identified using a novel secretion library technique in Escherichia coli
por: Kylväjä, Riikka, et al.
Publicado: (2011)

On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation
por: Wong, Wing-Cheong, et al.
Publicado: (2014)

Clustering evolving proteins into homologous families
por: Chan, Cheong Xin, et al.
Publicado: (2013)

Genome-Wide Analysis of Evolutionary Markers of Human Influenza A(H1N1)pdm09 and A(H3N2) Viruses May Guide Selection of Vaccine Strain Candidates
por: Belanov, Sergei S., et al.
Publicado: (2015)

A method of precise mRNA/DNA homology-based gene structure prediction
por: Churbanov, Alexander, et al.
Publicado: (2005)

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
por: Keilwagen, Jens, et al.
Publicado: (2018)

POXO: a web-enabled tool series to discover transcription factor binding sites
por: Kankainen, Matti, et al.
Publicado: (2006)

VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens
por: Garg, Aarti, et al.
Publicado: (2008)

Automated selection of homologs to track the evolutionary history of proteins
por: Mier, Pablo, et al.
Publicado: (2018)

Rapid generation of long tandem DNA repeat arrays by homologous recombination in yeast to study their function in mammalian genomes
por: Noskov, Vladimir N, et al.
Publicado: (2011)

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function
por: Törönen, Petri, et al.
Publicado: (2009)

Generation of Gene Ontology benchmark datasets with various types of positive signal
por: Törönen, Petri, et al.
Publicado: (2009)

Predicting functions of maize proteins using graph convolutional network
por: Zhou, Guangjie, et al.
Publicado: (2020)

An automated homology-based approach for identifying transposable elements
por: Kennedy, Ryan C, et al.
Publicado: (2011)

Physicochemical property distributions for accurate and rapid pairwise protein homology detection
por: Webb-Robertson, Bobbie-Jo M, et al.
Publicado: (2010)

Template-based prediction of protein structure with deep learning
por: Zhang, Haicang, et al.
Publicado: (2020)

Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data
por: Kilpinen, Sami K, et al.
Publicado: (2011)

Integrative approaches to the prediction of protein functions based on the feature selection
por: Ko, Seokha, et al.
Publicado: (2009)

Validity of self-reported out-of-school physical activity among Finnish 11-year-old children
por: Määttä, Suvi, et al.
Publicado: (2016)

Native flexibility of structurally homologous proteins: insights from anisotropic network model
por: Sarkar, Ranja
Publicado: (2017)

SANSparallel: interactive homology search against Uniprot
por: Somervuo, Panu, et al.
Publicado: (2015)

Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis
por: Frech, Christian, et al.
Publicado: (2009)

Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins
por: Neto, Armando de Menezes, et al.
Publicado: (2012)

GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction
por: Browne, Fiona, et al.
Publicado: (2009)

Homology-independent multiallelic disruption via CRISPR/Cas9-based knock-in yields distinct functional outcomes in human cells
por: Zhang, Chenzi, et al.
Publicado: (2018)

Protocol: Precision engineering of plant gene loci by homologous recombination cloning in Escherichia coli
por: Roden, Laura C, et al.
Publicado: (2005)

Improved prediction of critical residues for protein function based on network and phylogenetic analyses
por: Thibert, Boris, et al.
Publicado: (2005)

Ischemic Heart Disease Selectively Modifies the Right Atrial Appendage Transcriptome
por: Mulari, Severi, et al.
Publicado: (2021)

Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice
por: Wang, Xiyin, et al.
Publicado: (2006)

Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure
por: Abbass, Jad, et al.
Publicado: (2020)

Bacterial rose garden for metagenomic SNP-based phylogeny visualization
por: Alexeev, Dmitry, et al.
Publicado: (2015)

PredicTF: prediction of bacterial transcription factors in complex microbial communities using deep learning
por: Oliveira Monteiro, Lummy Maria, et al.
Publicado: (2022)

Incorporating functional inter-relationships into protein function prediction algorithms
por: Pandey, Gaurav, et al.
Publicado: (2009)

Dosimetrical and radiobiological approach to manage the dosimetric shift in the transition of dose calculation algorithm in radiation oncology: how to improve high quality treatment and avoid unexpected outcomes?
por: Chaikh, Abdulhamid, et al.
Publicado: (2018)

Homology building as a means to define antigenic epitopes on dihydrofolate reductase (DHFR) from Plasmodium falciparum
por: Alifrangis, Michael, et al.
Publicado: (2004)

PIKE-R2P: Protein–protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein prediction
por: Dai, Xinnan, et al.
Publicado: (2021)

BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing
por: Somervuo, Panu, et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_6s1k6cau24rfdggdl0rcumgenl