Non‐homology‐based prediction of gene functions in maize (Zea mays ssp. mays)
The Plant Genome, 2020 Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging.
Xiuru Dai +6 more
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Metagenomic annotation networks: construction and applications. [PDF]
PLoS ONE, 2012 The derivation and comparison of biological interaction networks are vital for understanding the functional capacity and hierarchical organization of integrated microbial communities.
Gregory Vey, Gabriel Moreno-Hagelsieb
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AnnotaPipeline: An integrated tool to annotate eukaryotic proteins using multi-omics data
Frontiers in Genetics, 2022 Assignment of gene function has been a crucial, laborious, and time-consuming step in genomics. Due to a variety of sequencing platforms that generates increasing amounts of data, manual annotation is no longer feasible. Thus, the need for an integrated,
Guilherme Augusto Maia +9 more
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Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation [PDF]
, 2014 Background Metatranscriptome sequence data can contain highly redundant sequences from diverse populations of microbes and so data reduction techniques are often applied before taxonomic and functional annotation.
Mock, Thomas +3 more
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DFLAT: functional annotation for human development [PDF]
BMC Bioinformatics, 2014 Recent increases in genomic studies of the developing human fetus and neonate have led to a need for widespread characterization of the functional roles of genes at different developmental stages. The Gene Ontology (GO), a valuable and widely-used resource for characterizing gene function, offers perhaps the most suitable functional annotation system ...
Wick, Heather C +8 more
openaire +3 more sources
FAPM: functional annotation of proteins using multimodal models beyond structural modeling. [PDF]
BioinformaticsXiang W +8 more
europepmc +3 more sources
Annotation extension through protein family annotation coherence metrics
Frontiers in Genetics, 2013 Protein functional annotation consists in associating proteins with textual descriptors elucidating their biological roles. The bulk of annotation is done via automated procedures that ultimately rely on annotation transfer.
Hugo Paulo Bastos +2 more
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htsint: a Python library for sequencing pipelines that combines data through gene set generation [PDF]
, 2015 Background: Sequencing technologies provide a wealth of details in terms of genes, expression, splice variants, polymorphisms, and other features. A standard for sequencing analysis pipelines is to put genomic or transcriptomic features into a context of
Bonneaud, Camille +2 more
core +3 more sources
Functional domain annotation by structural similarity
NAR Genomics and Bioinformatics, 2023 Abstract Traditional automated in silico functional annotation uses tools like Pfam that rely on sequence similarities for domain annotation. However, structural conservation often exceeds sequence conservation, suggesting an untapped potential for improved annotation through structural similarity. This approach was previously overlooked
Poorya Mirzavand Borujeni, Reza Salavati
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Gene3D: comprehensive structural and functional annotation of genomes [PDF]
, 2007 Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources.
A. Reid +24 more
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