scholarly journals JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison

2015 ◽  
Vol 32 (6) ◽  
pp. 929-931 ◽  
Author(s):  
Michael Richter ◽  
Ramon Rosselló-Móra ◽  
Frank Oliver Glöckner ◽  
Jörg Peplies
Keyword(s):  
Draft Genome ◽  
Web Server ◽  
Supplementary Information ◽  
Genome Comparison ◽  
Reference Database ◽  
Online Service ◽  
Genome Sequences ◽  
Species Circumscription ◽  
Correlation Search ◽  
User Friendly

Abstract Summary: JSpecies Web Server (JSpeciesWS) is a user-friendly online service for in silico calculating the extent of identity between two genomes, a parameter routinely used in the process of polyphasic microbial species circumscription. The service measures the average nucleotide identity (ANI) based on BLAST+ (ANIb) and MUMmer (ANIm), as well as correlation indexes of tetra-nucleotide signatures (Tetra). In addition, it provides a Tetra Correlation Search function, which allows to rapidly compare selected genomes against a continuously updated reference database with currently about 32 000 published whole and draft genome sequences. For comparison, own genomes can be uploaded and references can be selected from the JSpeciesWS reference database. The service indicates whether two genomes share genomic identities above or below the species embracing thresholds, and serves as a fast way to allocate unknown genomes in the frame of the hitherto sequenced species. Availability and implementation: JSpeciesWS is available at http://jspecies.ribohost.com/jspeciesws. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: [email protected]

scholarly journals OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species

2019 ◽  
Vol 47 (W1) ◽  
pp. W52-W58 ◽  
Author(s):  
Ling Xu ◽  
Zhaobin Dong ◽  
Lu Fang ◽  
Yongjiang Luo ◽  
Zhaoyuan Wei ◽  
...  
Keyword(s):  
Web Server ◽  
Venn Diagram ◽  
Orthologous Group ◽  
Genome Comparison ◽  
Species Number ◽  
Whole Genome ◽  
Functional Annotations ◽  
Occurrence Pattern ◽  
Multiple Species ◽  
User Friendly

Abstract OrthoVenn is a powerful web platform for the comparison and analysis of whole-genome orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new features that facilitate the comparative analysis of orthologous clusters among up to 12 species. Additionally, this update offers improvements to data visualization and interpretation, including an occurrence pattern table for interrogating the overlap of each orthologous group for the queried species. Within the occurrence table, the functional annotations and summaries of the disjunctions and intersections of clusters between the chosen species can be displayed through an interactive Venn diagram. To facilitate a broader range of comparisons, a larger number of species, including vertebrates, metazoa, protists, fungi, plants and bacteria, have been added in OrthoVenn2. Finally, a stand-alone version is available to perform large dataset comparisons and to visualize results locally without limitation of species number. In summary, OrthoVenn2 is an efficient and user-friendly web server freely accessible at https://orthovenn2.bioinfotoolkits.net.

scholarly journals Cell BLAST: Searching large-scale scRNA-seq databases via unbiased cell embedding

2019 ◽  
Author(s):  
Zhi-Jie Cao ◽  
Lin Wei ◽  
Shen Lu ◽  
De-Chang Yang ◽  
Ge Gao
Keyword(s):  
Real World ◽  
Large Scale ◽  
Web Server ◽  
Reference Database ◽  
Link Type ◽  
One Stop ◽  
User Friendly

AbstractAn effective and efficient cell-querying method is critical for integrating existing scRNA-seq data and annotating new data. Herein, we present Cell BLAST, an accurate and robust cell-querying method. Powered by a well-curated reference database and a user-friendly Web server, Cell BLAST (http://cblast.gao-lab.org) provides a one-stop solution for real-world scRNA-seq cell querying and annotation.

scholarly journals Diagnostic Sequences That Distinguish M. avium Subspecies Strains

2021 ◽  
Vol 7 ◽  
Author(s):  
John P. Bannantine ◽  
Judith R. Stabel ◽  
Darrell O. Bayles ◽  
Cyril Conde ◽  
Franck Biet
Keyword(s):  
Mycobacterium Avium ◽  
Draft Genome ◽  
Dna Amplification ◽  
Genomic Islands ◽  
Clinical Samples ◽  
Genome Comparison ◽  
Genome Sequences ◽  
Niche Adaptation ◽  
Comprehensive Comparison ◽  
Genome Context

Over a decade ago Mycobacterium avium subspecies paratuberculosis (Map) specific genes were initially identified in a whole genome context by comparing draft genome sequences of Map strain K-10 with Mycobacterium avium subspecies hominissuis (Mah) strain 104. This resulted in identification of 32 Map specific genes, not including repetitive elements, based on the two-genome comparison. The goal of this study was to define a more complete catalog of M. avium subspecies-specific genes. This is important for obtaining additional diagnostic targets for Johne's disease detection and for understanding the unique biology, evolution and niche adaptation of these organisms. There are now over 28 complete genome sequences representing three M. avium subspecies, including avium (Maa), Mah, and Map. We have conducted a comprehensive comparison of these genomes using two independent pan genomic comparison tools, PanOCT and Roary. This has led to the identification of more than 250 subspecies defining genes common to both analyses. The majority of these genes are arranged in clusters called genomic islands. We further reduced the number of diagnostic targets by excluding sequences having high BLAST similarity to other mycobacterial species recently added to the National Center for Biotechnology Information database. Genes identified as diagnostic following these bioinformatic approaches were further tested by DNA amplification PCR on an additional 20 M. avium subspecies strains. This combined approach confirmed 86 genes as Map-specific, seven as Maa-specific and three as Mah-specific. A single-tube PCR reaction was conducted as a proof of concept method to quickly distinguish M. avium subspecies strains. With these novel data, researchers can classify isolates in their freezers, quickly characterize clinical samples, and functionally analyze these unique genes.

scholarly journals SEABED: Small molEcule activity scanner weB servicE baseD

2014 ◽  
Vol 31 (5) ◽  
pp. 773-775 ◽  
Author(s):  
Carlos Fenollosa ◽  
Marcel Otón ◽  
Pau Andrio ◽  
Jorge Cortés ◽  
Modesto Orozco ◽  
...  
Keyword(s):  
Web Service ◽  
Web Server ◽  
Software As A Service ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Ensemble Docking ◽  
Web Tools ◽  
Protein Mutants ◽  
User Friendly ◽  
Hybrid Docking

Abstract Motivation: The SEABED web server integrates a variety of docking and QSAR techniques in a user-friendly environment. SEABED goes beyond the basic docking and QSAR web tools and implements extended functionalities like receptor preparation, library editing, flexible ensemble docking, hybrid docking/QSAR experiments or virtual screening on protein mutants. SEABED is not a monolithic workflow tool but Software as a Service platform. Availability and implementation: SEABED is a free web server available athttp://www.bsc.es/SEABED. No registration is required. Contact: [email protected] Supplementary information: Supplementary data are available atBioinformatics online.

scholarly journals AGP: A Multimethods Web Server for Alignment-Free Genome Phylogeny

2013 ◽  
Vol 30 (5) ◽  
pp. 1032-1037 ◽  
Author(s):  
Jinkui Cheng ◽  
Fuliang Cao ◽  
Zhihua Liu
Keyword(s):  
Web Server ◽  
Data Sets ◽  
Whole Genome ◽  
Alignment Method ◽  
Genome Sequences ◽  
Alignment Free ◽  
Tree Construction ◽  
Comparison Functions ◽  
Genome Phylogeny ◽  
User Friendly

Abstract Phylogenetic analysis based on alignment method meets huge challenges when dealing with whole-genome sequences, for example, recombination, shuffling, and rearrangement of sequences. Thus, various alignment-free methods for phylogeny construction have been proposed. However, most of these methods have not been implemented as tools or web servers. Researchers cannot use these methods easily with their data sets. To facilitate the usage of various alignment-free methods, we implemented most of the popular alignment-free methods and constructed a user-friendly web server for alignment-free genome phylogeny (AGP). AGP integrated the phylogenetic tree construction, visualization, and comparison functions together. Both AGP and all source code of the methods are available at http://www.herbbol.org:8000/agp (last accessed February 26, 2013). AGP will facilitate research in the field of whole-genome phylogeny and comparison.

scholarly journals MTR-Viewer: identifying regions within genes under purifying selection

2019 ◽  
Vol 47 (W1) ◽  
pp. W121-W126 ◽  
Author(s):  
Michael Silk ◽  
Slavé Petrovski ◽  
David B Ascher
Keyword(s):  
Selective Pressure ◽  
Web Server ◽  
Purifying Selection ◽  
Genome Sequences ◽  
Protein Coding ◽  
Sliding Windows ◽  
Alternative Transcripts ◽  
Missense Variation ◽  
User Friendly ◽  
Tolerance Ratio

Abstract Advances in genomic sequencing have enormous potential to revolutionize personalized medicine, however distinguishing disease-causing from benign variants remains a challenge. The increasing number of human genome and exome sequences available has revealed areas where unfavourable variation is removed through purifying selection. Here, we present the MTR-Viewer, a web-server enabling easy visualization at the gene or variant level of the Missense Tolerance Ratio (MTR), a measure of regional intolerance to missense variation calculated using variation from 240 000 exome and genome sequences. The MTR-Viewer enables exploration of MTR calculations, using different sliding windows, for over 18 000 human protein-coding genes and 85 000 alternative transcripts. Users can also view MTR scores calculated for specific ethnicities, to enable easy exploration of regions that may be under different selective pressure. The spatial distribution of population and known disease variants is also displayed on the protein's domain structure. Intolerant regions were found to be highly enriched for ClinVar pathogenic and COSMIC somatic missense variants (Mann–Whitney U test P < 2.2 × 10−16). As the MTR is not biased by known domains and protein features, it can highlight functionally important regions within genes overlooked or inaccessible by traditional methods. MTR-Viewer is freely available via a user friendly web-server at http://biosig.unimelb.edu.au/mtr-viewer/.

PlncRNADB: A Repository of Plant lncRNAs and lncRNA-RBP Protein Interactions

2019 ◽  
Vol 14 (7) ◽  
pp. 621-627 ◽  
Author(s):  
Youhuang Bai ◽  
Xiaozhuan Dai ◽  
Tiantian Ye ◽  
Peijing Zhang ◽  
Xu Yan ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Populus Trichocarpa ◽  
Noncoding Rnas ◽  
Reference Database ◽  
Protein Coding ◽  
Arabidopsis Lyrata ◽  
User Friendly

Background: Long noncoding RNAs (lncRNAs) are endogenous noncoding RNAs, arbitrarily longer than 200 nucleotides, that play critical roles in diverse biological processes. LncRNAs exist in different genomes ranging from animals to plants. Objective: PlncRNADB is a searchable database of lncRNA sequences and annotation in plants. Methods: We built a pipeline for lncRNA prediction in plants, providing a convenient utility for users to quickly distinguish potential noncoding RNAs from protein-coding transcripts. Results: More than five thousand lncRNAs are collected from four plant species (Arabidopsis thaliana, Arabidopsis lyrata, Populus trichocarpa and Zea mays) in PlncRNADB. Moreover, our database provides the relationship between lncRNAs and various RNA-binding proteins (RBPs), which can be displayed through a user-friendly web interface. Conclusion: PlncRNADB can serve as a reference database to investigate the lncRNAs and their interaction with RNA-binding proteins in plants. The PlncRNADB is freely available at http://bis.zju.edu.cn/PlncRNADB/.

scholarly journals Draft Genome Sequences of 12 Mycolicibacterium smegmatis Strains Resistant to Imidazo[1,2-b][1,2,4,5]Tetrazines

2019 ◽  
Vol 8 (16) ◽  
Author(s):  
Aleksey A. Vatlin ◽  
Kirill V. Shur ◽  
Valery N. Danilenko ◽  
Dmitry A. Maslov
Keyword(s):  
Draft Genome ◽  
Transcriptional Repressor ◽  
Antituberculosis Drug ◽  
Genome Sequences ◽  
Content Type ◽  
Drug Candidates

Here, we report 12 draft genome sequences of mutant Mycolicibacterium smegmatis strains resistant to imidazo[1,2-b][1,2,4,5]tetrazines, which are antituberculosis drug candidates. We have identified 7 different mutations in the MSMEG_1380 gene, which encodes the AcrR/TetR_N transcriptional repressor, which may activate efflux-mediated resistance.

scholarly journals Draft Genome Sequences of Three Flavobacterium psychrophilum Strains Isolated from Diseased Ayu (Plecoglossus altivelis altivelis) Caught at Three Sites in the Kagami River in Kochi, Japan

2019 ◽  
Vol 8 (34) ◽  
Author(s):  
Hazuki Yamashita ◽  
Takayuki Wada ◽  
Yusuke Kato ◽  
Takuji Ikeda ◽  
Masayuki Imajoh
Keyword(s):  
Draft Genome ◽  
Psychrophilic Bacterium ◽  
Genome Sequences ◽  
Plecoglossus Altivelis ◽  
Gram Negative ◽  
Content Type ◽  
Flavobacterium Psychrophilum ◽  
Skin Ulcers ◽  
The Family

Flavobacterium psychrophilum is a Gram-negative, psychrophilic bacterium within the family Flavobacteriaceae. Here, we report the draft genome sequences of three F. psychrophilum strains isolated from skin ulcers of diseased ayu caught by tomozuri angling at three sites in the Kagami River in Japan.

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