cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters

AbstractGenes involved in coordinated biological pathways, including metabolism, drug resistance and virulence, are often collocalised as gene clusters. Identifying homologous gene clusters aids in the study of their function and evolution, however existing tools are limited to searching local sequence databases. Tools for remotely searching public databases are necessary to keep pace with the rapid growth of online genomic data. Here, we present cblaster, a Python based tool to rapidly detect collocated genes in local and remote databases. cblaster is easy to use, offering both a command line and a user-friendly graphical user interface (GUI). It generates outputs that enable intuitive visualisations of large datasets, and can be readily incorporated into larger bioinformatic pipelines. cblaster is a significant update to the comparative genomics toolbox. cblaster source code and documentation is freely available from GitHub under the MIT license (github.com/gamcil/cblaster).

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Gcluster: a simple-to-use tool for visualizing and comparing genome contexts for numerous genomes

Bioinformatics ◽

10.1093/bioinformatics/btaa212 ◽

2020 ◽

Vol 36 (12) ◽

pp. 3871-3873 ◽

Cited By ~ 1

Author(s):

Xiangyang Li ◽

Fang Chen ◽

Yunpeng Chen

Keyword(s):

Source Code ◽

Gene Clusters ◽

Genomic Region ◽

Supplementary Information ◽

Homologous Gene ◽

High Quality ◽

Large Numbers ◽

Linear Maps ◽

User Friendly

Abstract Motivation Comparing the organization of gene, gene clusters and their flanking genomic contexts is of critical importance to the determination of gene function and evolutionary basis of microbial traits. Currently, user-friendly and flexible tools enabling to visualize and compare genomic contexts for numerous genomes are still missing. Results We here present Gcluster, a stand-alone Perl tool that allows researchers to customize and create high-quality linear maps of the genomic region around the genes of interest across large numbers of completed and draft genomes. Importantly, Gcluster integrates homologous gene analysis, in the form of a built-in orthoMCL, and mapping genomes onto a given phylogeny to provide superior comparison of gene contexts. Availability and implementation Gcluster is written in Perl and released under GPLv3. The source code is freely available at https://github.com/Xiangyang1984/Gcluster and http://www.microbialgenomic.com/Gcluster_tool.html. Gcluster can also be installed through conda: ‘conda install -c bioconda gcluster’. Supplementary information Supplementary data are available at Bioinformatics online.

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Recent developments in theCCP-EMsoftware suite

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798317007859 ◽

2017 ◽

Vol 73 (6) ◽

pp. 469-477 ◽

Cited By ~ 101

Author(s):

Tom Burnley ◽

Colin M. Palmer ◽

Martyn Winn

Keyword(s):

Easy Access ◽

Software Framework ◽

Command Line ◽

Command Line Interface ◽

Software Suite ◽

Computational Support ◽

Recent Developments ◽

User Friendly ◽

Different Levels ◽

Friendly Graphical User Interface

As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessibleviaa user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The currentCCP-EMsuite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail.

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DamageProfiler: Fast damage pattern calculation for ancient DNA

Bioinformatics ◽

10.1093/bioinformatics/btab190 ◽

2021 ◽

Author(s):

Judith Neukamm ◽

Alexander Peltzer ◽

Kay Nieselt

Keyword(s):

Ancient Dna ◽

Source Code ◽

Supplementary Information ◽

Command Line ◽

Central Importance ◽

Command Line Interface ◽

Analysis Pipeline ◽

File Formats ◽

Programming Knowledge ◽

User Friendly

Abstract Motivation In ancient DNA research, the authentication of ancient samples based on specific features remains a crucial step in data analysis. Because of this central importance, researchers lacking deeper programming knowledge should be able to run a basic damage authentication analysis. Such software should be user-friendly and easy to integrate into an analysis pipeline. Results DamageProfiler is a Java based, stand-alone software to determine damage patterns in ancient DNA. The results are provided in various file formats and plots for further processing. DamageProfiler has an intuitive graphical as well as command line interface that allows the tool to be easily embedded into an analysis pipeline. Availability All of the source code is freely available on GitHub (https://github.com/Integrative-Transcriptomics/DamageProfiler). Supplementary information Supplementary data are available at Bioinformatics online.

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ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiota

10.1101/183970 ◽

2017 ◽

Cited By ~ 2

Author(s):

Bérénice Batut ◽

Kévin Gravouil ◽

Clémence Defois ◽

Saskia Hiltemann ◽

Jean-François Brugère ◽

...

Keyword(s):

Technological Progress ◽

Source Code ◽

Command Line ◽

Bioinformatic Tools ◽

Link Type ◽

Data Analyses ◽

The Galaxy ◽

Sequencing Platforms ◽

User Friendly ◽

New Generation

AbstractBackgroundNew generation of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies.FindingsWe therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides a curated collection of tools to explore and visualize taxonomic and functional information from raw amplicon, metagenomic or metatranscriptomic sequences. To guide different analyses, several customizable workflows are included. All workflows are supported by tutorials and Galaxy interactive tours to guide the users through the analyses step by step. ASaiM is implemented as Galaxy Docker flavour. It is scalable to many thousand datasets, but also can be used a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io/)ConclusionsBased on the Galaxy framework, ASaiM offers sophisticated analyses to scientists without command-line knowledge. ASaiM provides a powerful framework to easily and quickly explore microbiota data in a reproducible and transparent environment.

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Development of graphical user interface for open source VLSI digital synthesis tool Qflow

International Journal of Engineering & Technology ◽

10.14419/ijet.v7i1.1.12649 ◽

2018 ◽

Vol 7 (2) ◽

pp. 710

Author(s):

K. Sripath Roy ◽

K. Abhiram ◽

M. Arun Sumanth ◽

Jaishree Jaishankar ◽

P. Abhishek ◽

...

Keyword(s):

User Interface ◽

Open Source ◽

Graphical User Interface ◽

Source Code ◽

Command Line ◽

Simulation Process ◽

Vlsi Technology ◽

Synthesis Tool ◽

Digital Synthesis ◽

User Friendly

There are many tools that are used for simulation in the domain of VLSI technology but none of them are easily accessible. There is a need for Free and open source tools in this stream so as to make them accessible to everyone. There are efficient tools that already exist in open source in VLSI stream but are not used widely because of their command line user interface. Hence, creating a user friendly interface will help many developers and users to work easily. This paper deals with the idea to solve the above issue by creating a Graphical User Interface for the open source VLSI tool called QFlow. Qflow is a tool used in synthesizing a VLSI circuit from the Verilog source code. There are multiple tools integrated with this tool to assure the simulation process. It is a combination of many dependencies that are used for synthesis, placement, layout viewing and routing in a fabrication process. All the independent tools used for the Verilog code simulation are integrated onto a single platform. Qt is used for creating the cross-stage application.

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tspex: a tissue-specificity calculator for gene expression data

10.21203/rs.3.rs-51998/v1 ◽

2020 ◽

Author(s):

Antonio P. Camargo ◽

Adrielle A. Vasconcelos ◽

Mateus B. Fiamenghi ◽

Gonçalo A. G. Pereira ◽

Marcelo F. Carazzolle

Keyword(s):

Gene Expression ◽

Gene Expression Data ◽

Web Application ◽

Tissue Specificity ◽

Source Code ◽

Command Line ◽

Expression Data ◽

Web Interface ◽

User Friendly ◽

Different Tissues

Abstract When comparing gene expression data of different tissues it is often interesting to identify tissue-specific genes or transcripts. Even though there are several metrics to measure tissue-specificity, a user-friendly tool that facilitates this analysis is not available yet. We present tspex, a software that allows easy computation of a comprehensive set of different tissue-specificity metrics from gene expression data. tspex can be used through a web interface, command-line or the Python API. Its package version also provides visualization functions that facilitate inspection of results. The documentation and the source code of tspex are available at https://apcamargo.github.io/tspex/ and the web application can be accessed at https://tspex.lge.ibi.unicamp.br/

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Identification, heterologous production and bioactivity of lentinulin A and dendrothelin A, two natural variants of backbone N-methylated peptide macrocycle omphalotin A

Scientific Reports ◽

10.1038/s41598-021-83106-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Emmanuel Matabaro ◽

Hannelore Kaspar ◽

Paul Dahlin ◽

Daniel L. V. Bader ◽

Claudia E. Murar ◽

...

Keyword(s):

Natural Products ◽

Lentinula Edodes ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Precursor Protein ◽

Fungal Genome ◽

Homologous Gene ◽

C Terminus ◽

Natural Variants ◽

Recombinant Peptides

AbstractBackbone N-methylation and macrocyclization improve the pharmacological properties of peptides by enhancing their proteolytic stability, membrane permeability and target selectivity. Borosins are backbone N-methylated peptide macrocycles derived from a precursor protein which contains a peptide α-N-methyltransferase domain autocatalytically modifying the core peptide located at its C-terminus. Founding members of borosins are the omphalotins from the mushroom Omphalotus olearius (omphalotins A-I) with nine out of 12 L-amino acids being backbone N-methylated. The omphalotin biosynthetic gene cluster codes for the precursor protein OphMA, the protease prolyloligopeptidase OphP and other proteins that are likely to be involved in other post-translational modifications of the peptide. Mining of available fungal genome sequences revealed the existence of highly homologous gene clusters in the basidiomycetes Lentinula edodes and Dendrothele bispora. The respective borosins, referred to as lentinulins and dendrothelins are naturally produced by L. edodes and D. bispora as shown by analysis of respective mycelial extracts. We produced all three homologous peptide natural products by coexpression of OphMA hybrid proteins and OphP in the yeast Pichia pastoris. The recombinant peptides differ in their nematotoxic activity against the plant pathogen Meloidogyne incognita. Our findings pave the way for the production of borosin peptide natural products and their potential application as novel biopharmaceuticals and biopesticides.

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Two User-Friendly Molecular Markers Developed for the Identification of Hybrid Lethality Genes in Brassica oleracea

Agronomy ◽

10.3390/agronomy11050982 ◽

2021 ◽

Vol 11 (5) ◽

pp. 982

Author(s):

Zhiliang Xiao ◽

Congcong Kong ◽

Fengqing Han ◽

Limei Yang ◽

Mu Zhuang ◽

...

Keyword(s):

Molecular Markers ◽

Brassica Oleracea ◽

Rapid Identification ◽

Inbred Lines ◽

Hybrid Lethality ◽

Specific Pcr ◽

Allele Specific ◽

User Friendly ◽

Allele Specific Pcr ◽

Kasp Marker

Cabbage (Brassica oleracea) is an important vegetable crop that is cultivated worldwide. Previously, we reported the identification of two dominant complementary hybrid lethality (HL) genes in cabbage that could result in the death of hybrids. To avoid such losses in the breeding process, we attempted to develop molecular markers to identify HL lines. Among 54 previous mapping markers closely linked to BoHL1 or BoHL2, only six markers for BoHL2 were available in eight cabbage lines (two BoHL1 lines; three BoHL2 lines; three lines without BoHL); however, they were neither universal nor user-friendly in more inbred lines. To develop more accurate markers, these cabbage lines were resequenced at an ~20× depth to obtain more nucleotide variations in the mapping regions. Then, an InDel in BoHL1 and a single-nucleotide polymorphism (SNP) in BoHL2 were identified, and the corresponding InDel marker MBoHL1 and the competitive allele-specific PCR (KASP) marker KBoHL2 were developed and showed 100% accuracy in eight inbred lines. Moreover, we identified 138 cabbage lines using the two markers, among which one inbred line carried BoHL1 and 11 inbred lines carried BoHL2. All of the lethal line genotypes obtained with the two markers matched the phenotype. Two markers were highly reliable for the rapid identification of HL genes in cabbage.

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Biofilm Formation in Pseudomonas aeruginosa: Fimbrial cup Gene Clusters Are Controlled by the Transcriptional Regulator MvaT

Journal of Bacteriology ◽

10.1128/jb.186.9.2880-2890.2004 ◽

2004 ◽

Vol 186 (9) ◽

pp. 2880-2890 ◽

Cited By ~ 102

Author(s):

Isabelle Vallet ◽

Stephen P. Diggle ◽

Rachael E. Stacey ◽

Miguel Cámara ◽

Isabelle Ventre ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Biofilm Formation ◽

Dna Microarrays ◽

Transcriptional Profiling ◽

Bacterial Pathogen ◽

Gene Clusters ◽

Northern Blotting ◽

Negative Regulator ◽

Regulatory Control ◽

Homologous Gene

ABSTRACT Pseudomonas aeruginosa is an opportunistic bacterial pathogen which poses a major threat to long-term-hospitalized patients and individuals with cystic fibrosis. The capacity of P. aeruginosa to form biofilms is an important requirement for chronic colonization of human tissues and for persistence in implanted medical devices. Various stages of biofilm formation by this organism are mediated by extracellular appendages, such as type IV pili and flagella. Recently, we identified three P. aeruginosa gene clusters that were termed cup (chaperone-usher pathway) based on their sequence relatedness to the chaperone-usher fimbrial assembly pathway in other bacteria. The cupA gene cluster, but not the cupB or cupC cluster, is required for biofilm formation on abiotic surfaces. In this study, we identified a gene (mvaT) encoding a negative regulator of cupA expression. Such regulatory control was confirmed by several approaches, including lacZ transcriptional fusions, Northern blotting, and transcriptional profiling using DNA microarrays. MvaT also represses the expression of the cupB and cupC genes, although the extent of the regulatory effect is not as pronounced as with cupA. Consistent with this finding, mvaT mutants exhibit enhanced biofilm formation. Although the P. aeruginosa genome contains a highly homologous gene, mvaU, the repression of cupA genes is MvaT specific. Thus, MvaT appears to be an important regulatory component within a complex network that controls biofilm formation and maturation in P. aeruginosa.

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Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files

Cancer Informatics ◽

10.4137/cin.s26470 ◽

2015 ◽

Vol 14 ◽

pp. CIN.S26470 ◽

Cited By ~ 2

Author(s):

Richard P. Finney ◽

Qing-Rong Chen ◽

Cu V. Nguyen ◽

Chih Hao Hsu ◽

Chunhua Yan ◽

...

Keyword(s):

Graphical User Interface ◽

Reference Genome ◽

Source Code ◽

Software Tool ◽

Command Line ◽

Sequencing Data ◽

Genome Data ◽

Command Line Tool ◽

Portable Software ◽

Microsoft Windows

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview . The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview .

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