scholarly journals Bioinformatic approaches for functional annotation and pathway inference in metagenomics data

2012 ◽  
Vol 13 (6) ◽  
pp. 696-710 ◽  
Author(s):  
C. De Filippo ◽  
M. Ramazzotti ◽  
P. Fontana ◽  
D. Cavalieri
Keyword(s):  
Functional Annotation ◽  
Pathway Inference ◽  
Metagenomics Data ◽  
Bioinformatic Approaches

scholarly journals GOsummaries: an R Package for Visual Functional Annotation of Experimental Data

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 574 ◽  
Author(s):  
Raivo Kolde ◽  
Jaak Vilo
Keyword(s):  
Experimental Data ◽  
Functional Annotation ◽  
Principal Component ◽  
Enrichment Analysis ◽  
R Package ◽  
Functional Characterisation ◽  
Go Enrichment ◽  
Word Clouds ◽  
Single List ◽  
Metagenomics Data

Functional characterisation of gene lists using Gene Ontology (GO) enrichment analysis is a common approach in computational biology, since many analysis methods end up with a list of genes as a result. Often there can be hundreds of functional terms that are significantly associated with a single list of genes and proper interpretation of such results can be a challenging endeavour. There are methods to visualise and aid the interpretation of these results, but most of them are limited to the results associated with one list of genes. However, in practice the number of gene lists can be considerably higher and common tools are not effective in such situations.We introduce a novel R package, 'GOsummaries' that visualises the GO enrichment results as concise word clouds that can be combined together if the number of gene lists is larger. By also adding the graphs of corresponding raw experimental data, GOsummaries can create informative summary plots for various analyses such as differential expression or clustering. The case studies show that the GOsummaries plots allow rapid functional characterisation of complex sets of gene lists. The GOsummaries approach is particularly effective for Principal Component Analysis (PCA).By adding functional annotation to the principal components, GOsummaries improves  significantly the interpretability of PCA results. The GOsummaries layout for PCA can be effective even in situations where we cannot directly apply the GO analysis. For example, in case of metabolomics or metagenomics data it is possible to show the features with significant associations to the components instead of GO terms.  The GOsummaries package is available under GPL-2 licence at Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/GOsummaries.html).

scholarly journals A most wanted list of conserved protein families with no known domains

2017 ◽  
Author(s):  
Stacia K. Wyman ◽  
Aram Avila-Herrera ◽  
Stephen Nayfach ◽  
Katherine S. Pollard
Keyword(s):  
Functional Annotation ◽  
Functional Characterization ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Protein Domain ◽  
Protein Families ◽  
Bioinformatics Pipeline ◽  
Metagenomics Data ◽  
Sequence Databases

AbstractThe number and proportion of genes with no known function are growing rapidly. To quantify this phenomenon and provide criteria for prioritizing genes for functional characterization, we developed a bioinformatics pipeline that identifies robustly defined protein families with no annotated domains, ranks these with respect to phylogenetic breadth, and identifies them in metagenomics data. We applied this approach to 271 965 protein families from the SFams database and discovered many with no functional annotation, including >118 000 families lacking any known protein domain. From these, we prioritized 6 668 conserved protein families with at least three sequences from organisms in at least two distinct classes. These Function Unknown Families (FUnkFams) are present in Tara Oceans Expedition and Human Microbiome Project metagenomes, with distributions associated with sampling environment. Our findings highlight the extent of functional novelty in sequence databases and establish an approach for creating a “most wanted” list of genes to characterize.

Functional Annotation of Genes of Predisposition to Schizophrenia and Celiac Disease

2020 ◽  
Vol 56 (10) ◽  
pp. 1246-1251
Author(s):  
N. Yu. Chasovskikh ◽  
A. Yu. Grechishnikova
Keyword(s):  
Celiac Disease ◽  
Functional Annotation

scholarly journals De Novo Sporophyte Transcriptome Assembly and Functional Annotation in the Endangered Fern Species Vandenboschia speciosa (Willd.) G. Kunkel

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1017
Author(s):  
Mohammed Bakkali ◽  
Rubén Martín-Blázquez ◽  
Mercedes Ruiz-Estévez ◽  
Manuel A. Garrido-Ramos
Keyword(s):  
Functional Annotation ◽  
Vascular Plants ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Systematic Position ◽  
Important Data ◽  
Ecological Requirements ◽  
Physiological Adaptations ◽  
Fern Species ◽  
Go Terms

We sequenced the sporophyte transcriptome of Killarney fern (Vandenboschia speciosa (Willd.) G. Kunkel). In addition to being a rare endangered Macaronesian-European endemism, this species has a huge genome (10.52 Gb) as well as particular biological features and extreme ecological requirements. These characteristics, together with the systematic position of ferns among vascular plants, make it of high interest for evolutionary, conservation and functional genomics studies. The transcriptome was constructed de novo and contained 36,430 transcripts, of which 17,706 had valid BLAST hits. A total of 19,539 transcripts showed at least one of the 7362 GO terms assigned to the transcriptome, whereas 6547 transcripts showed at least one of the 1359 KEGG assigned terms. A prospective analysis of functional annotation results provided relevant insights on genes involved in important functions such as growth and development as well as physiological adaptations. In this context, a catalogue of genes involved in the genetic control of plant development, during the vegetative to reproductive transition, in stress response as well as genes coding for transcription factors is given. Altogether, this study provides a first step towards understanding the gene expression of a significant fern species and the in silico functional and comparative analyses reported here provide important data and insights for further comparative evolutionary studies in ferns and land plants in general.

scholarly journals Recent advances in CRISPR/Cas9 and applications for wheat functional genomics and breeding

aBIOTECH ◽  
2021 ◽  
Author(s):  
Jun Li ◽  
Yan Li ◽  
Ligeng Ma
Keyword(s):  
Functional Genomics ◽  
Genome Editing ◽  
Functional Annotation ◽  
Genome Engineering ◽  
Agronomic Traits ◽  
Wheat Breeding ◽  
Breeding Programs ◽  
Base Editing ◽  
The World ◽  
World Food Security

AbstractCommon wheat (Triticum aestivum L.) is one of the three major food crops in the world; thus, wheat breeding programs are important for world food security. Characterizing the genes that control important agronomic traits and finding new ways to alter them are necessary to improve wheat breeding. Functional genomics and breeding in polyploid wheat has been greatly accelerated by the advent of several powerful tools, especially CRISPR/Cas9 genome editing technology, which allows multiplex genome engineering. Here, we describe the development of CRISPR/Cas9, which has revolutionized the field of genome editing. In addition, we emphasize technological breakthroughs (e.g., base editing and prime editing) based on CRISPR/Cas9. We also summarize recent applications and advances in the functional annotation and breeding of wheat, and we introduce the production of CRISPR-edited DNA-free wheat. Combined with other achievements, CRISPR and CRISPR-based genome editing will speed progress in wheat biology and promote sustainable agriculture.

Structural characterization and functional annotation of microbial proteases mined from solid tannery waste metagenome

Biologia ◽  
2021 ◽  
Author(s):  
Sumit K. Verma ◽  
Simerpreet Kaur ◽  
Arnav Tevetia ◽  
Sayan Chatterjee ◽  
Prakash C. Sharma
Keyword(s):  
Structural Characterization ◽  
Functional Annotation ◽  
Tannery Waste

scholarly journals CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

2020 ◽  
Author(s):  
Matteo Chiara ◽  
Federico Zambelli ◽  
Marco Antonio Tangaro ◽  
Pietro Mandreoli ◽  
David S Horner ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Ad Hoc ◽  
State Of The Art ◽  
Supplementary Information ◽  
Genomic Sequences ◽  
Supplementary Data ◽  
Evolutionary Patterns ◽  
Genomic Variants ◽  
Art Methods ◽  
Available Resources

Abstract Summary While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2. Availabilityand implementation Galaxy   http://corgat.cloud.ba.infn.it/galaxy; software: https://github.com/matteo14c/CorGAT/tree/Revision_V1; docker: https://hub.docker.com/r/laniakeacloud/galaxy_corgat. Supplementary information Supplementary data are available at Bioinformatics online.

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