AIMC Topic: Molecular Sequence Annotation

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Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences.

Genomics Apr 8, 2015
Functional annotation of the gigantic metagenomic data is one of the major time-consuming and computationally demanding tasks, which is currently a bottleneck for the efficient analysis. The commonly used homology-based methods to functionally annota...
Humans Proteins Metagenomics Molecular Sequence Annotation Sequence Analysis, Protein Machine Learning Software Genomics
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Assessing the effects of data selection and representation on the development of reliable E. coli sigma 70 promoter region predictors.

PloS one Mar 24, 2015
As the number of sequenced bacterial genomes increases, the need for rapid and reliable tools for the annotation of functional elements (e.g., transcriptional regulatory elements) becomes more desirable. Promoters are the key regulatory elements, whi...
Molecular Sequence Annotation DNA-Directed RNA Polymerases Sigma Factor Escherichia coli Machine Learning Base Sequence Algorithms Promoter Regions, Genetic Computational Biology
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De novo transcriptome assembly of pummelo and molecular marker development.

PloS one Mar 23, 2015
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtai...
Genetic Markers High-Throughput Nucleotide Sequencing Gene Frequency Citrus Transcriptome Polymorphism, Single Nucleotide Cluster Analysis Phylogeny Gene Library Molecular Sequence Annotation Gene Expression Profiling Phenotype Microsatellite Repeats Gene Ontology Physical Chromosome Mapping Reproducibility of Results Nucleotide Motifs
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GRYFUN: a web application for GO term annotation visualization and analysis in protein sets.

PloS one Mar 20, 2015
Functional context for biological sequence is provided in the form of annotations. However, within a group of similar sequences there can be annotation heterogeneity in terms of coverage and specificity. This in turn can introduce issues regarding th...
Molecular Sequence Annotation Gene Ontology Web Browser Computational Biology Databases, Protein Datasets as Topic Software
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Integrating biological knowledge based on functional annotations for biclustering of gene expression data.

Computer methods and programs in biomedicine Mar 18, 2015
Gene expression data analysis is based on the assumption that co-expressed genes imply co-regulated genes. This assumption is being reformulated because the co-expression of a group of genes may be the result of an independent activation with respect...
Genes, Fungal Molecular Sequence Annotation Algorithms Gene Ontology Cluster Analysis Knowledge Bases Unsupervised Machine Learning Data Mining Gene Expression Profiling Yeasts Databases, Genetic
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Ontology application and use at the ENCODE DCC.

Database : the journal of biological databases and curation Mar 16, 2015
The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a catalog of genomic annotations. To date, the project has generated over 4000 experiments across more than 350 cell lines and tissues using a wide array o...
Data Curation Transcription, Genetic Animals Humans Gene Regulatory Networks Databases, Genetic Gene Ontology Mice Molecular Sequence Annotation
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Choose wisely: Network, ontology and annotation resources for the analysis of Staphylococcus aureus omics data.

International journal of medical microbiology : IJMM Feb 14, 2015
Staphylococcus aureus (S. aureus) is a prominent human and livestock pathogen investigated widely using omic technologies. Critically, due to availability, low visibility or scattered resources, robust network and statistical contextualisation of the...
Molecular Sequence Annotation Gene Ontology Humans Gene Regulatory Networks Computational Biology Staphylococcus aureus
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Measuring semantic similarities by combining gene ontology annotations and gene co-function networks.

BMC bioinformatics Feb 14, 2015
BACKGROUND: Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based similarity because of the li...
Humans Software Algorithms Gene Regulatory Networks Cytochrome P-450 Enzyme System Semantics Vocabulary, Controlled Molecular Sequence Annotation Computational Biology Metabolic Networks and Pathways Multigene Family Gene Ontology Saccharomyces cerevisiae Proteins Arabidopsis Proteins
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RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Science (New York, N.Y.) Dec 18, 2014
To facilitate precision medicine and whole-genome annotation, we developed a machine-learning technique that scores how strongly genetic variants affect RNA splicing, whose alteration contributes to many diseases. Analysis of more than 650,000 intron...
Muscular Atrophy, Spinal Exons Genetic Code MutL Protein Homolog 1 RNA Splice Sites RNA Splicing Child Development Disorders, Pervasive Colorectal Neoplasms, Hereditary Nonpolyposis Introns Mutation, Missense Quantitative Trait Loci Models, Genetic Nuclear Proteins Adaptor Proteins, Signal Transducing Genetic Variation Molecular Sequence Annotation DNA Genetic Markers Humans Artificial Intelligence Polymorphism, Single Nucleotide Computer Simulation RNA-Binding Proteins Genome-Wide Association Study
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Gene Ontology Consortium: going forward.

Nucleic acids research Nov 26, 2014
The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to...
Cell Cycle Molecular Sequence Annotation Gene Ontology Databases, Genetic Internet
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