<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/35395?offset=120 https://bioinformaticsonline.com/bookmarks/view/44518/virus-bioinformatics-tools Wed, 24 Apr 2024 06:19:55 -0500 https://bioinformaticsonline.com/bookmarks/view/44518/virus-bioinformatics-tools <![CDATA[Virus Bioinformatics Tools]]> Bioinformatics tools play a crucial role in studying viruses, enabling researchers to analyze their genetic makeup, structure, function, and evolution. Here are some commonly used bioinformatics tools for virus research

https://evirusbioinfc.notion.site/18e21bc49827484b8a2f84463cb40b8d?v=92e7eb6703be4720abf17a901bc9a947

Address of the bookmark: https://evirusbioinfc.notion.site/18e21bc49827484b8a2f84463cb40b8d?v=92e7eb6703be4720abf17a901bc9a947

]]> LEGE https://bioinformaticsonline.com/blog/view/44718/mycology-research-resources-for-bioinformaticians-unlocking-the-fungal-kingdom Fri, 13 Dec 2024 11:21:45 -0600 https://bioinformaticsonline.com/blog/view/44718/mycology-research-resources-for-bioinformaticians-unlocking-the-fungal-kingdom <![CDATA[Mycology Research Resources for Bioinformaticians: Unlocking the Fungal Kingdom]]> Mycology, the study of fungi, is a field that bridges ecology, medicine, and biotechnology. With advancements in bioinformatics, researchers now have unprecedented opportunities to explore the fungal kingdom at molecular, genetic, and ecological levels. From understanding pathogenic fungi to harnessing fungal enzymes for industrial applications, the potential is vast.

To fully leverage these opportunities, bioinformaticians require specialized tools and databases. This blog highlights essential resources for mycology research, focusing on databases, tools, and platforms tailored for fungal biology.

1. Fungal Databases

1.1. MycoCosm

Website: MycoCosm
Developed by the DOE Joint Genome Institute, MycoCosm is a comprehensive portal for fungal genomics. It offers genomic and transcriptomic data for a wide range of fungi, including saprobes, pathogens, and symbionts.

  • Key Features: Genome browsers, comparative genomics tools, and functional annotations.
  • Best For: Large-scale studies on fungal evolution and ecology.
1.2. FungiDB

Website: FungiDB
FungiDB is an integrated genomic resource for fungal pathogens and non-pathogens. It provides access to genome sequences, transcriptomic data, and functional annotations.

  • Key Features: Advanced search options, BLAST, and pathway analysis tools.
  • Best For: Studying fungal pathogenesis and host-pathogen interactions.
1.3. Index Fungorum

Website: Index Fungorum
This nomenclatural database provides information on the scientific names of fungi. It’s an essential resource for taxonomists and researchers focused on fungal biodiversity.

  • Key Features: Taxonomic hierarchy and synonymy tracking.
  • Best For: Identifying and classifying fungal species.
1.4. UNITE

Website: UNITE
UNITE is a specialized database for fungal ITS (Internal Transcribed Spacer) sequences, often used in fungal identification and phylogenetics.

  • Key Features: Curated reference datasets and community annotations.
  • Best For: Environmental mycology and microbial ecology studies.

2. Analytical Tools

2.1. Funannotate

Repository: GitHub - Funannotate
Funannotate is a genome annotation tool designed for fungi. It supports tasks like gene prediction, functional annotation, and orthology analysis.

  • Best For: Annotating newly sequenced fungal genomes.
2.2. BUSCO (Benchmarking Universal Single-Copy Orthologs)

Website: BUSCO
BUSCO evaluates genome assembly and annotation completeness using orthologs. It includes a fungal-specific dataset.

  • Best For: Assessing the quality of fungal genome assemblies.
2.3. Pathogen-Host Interactions Database (PHI-base)

Website: PHI-base
PHI-base is a manually curated resource containing information on pathogen-host interactions, including fungal pathogens.

  • Best For: Exploring virulence factors and host-pathogen relationships.

3. Visualization Platforms

3.1. Cytoscape

Website: Cytoscape
A powerful tool for visualizing molecular interaction networks, Cytoscape can be used to study protein-protein interactions, gene networks, and metabolic pathways in fungi.

  • Best For: Network biology and functional genomics.
3.2. iTOL (Interactive Tree of Life)

Website: iTOL
iTOL is an interactive tool for visualizing phylogenetic trees.

  • Best For: Displaying fungal phylogenies and comparing evolutionary relationships.

4. Community Resources

4.1. Mycological Society of America (MSA)

Website: MSA
The MSA promotes fungal research and provides access to resources, conferences, and publications.

  • Best For: Networking with fungal researchers and accessing recent studies.
4.2. OpenFungi

Website: OpenFungi
OpenFungi is an open-source initiative providing fungal genomic and transcriptomic datasets for research and education.

  • Best For: Sharing and accessing public fungal datasets.

5. Genomics Workflows

5.1. Galaxy

Website: Galaxy Project
Galaxy offers a web-based platform for reproducible bioinformatics workflows, including tools for fungal genome and transcriptome analysis.

  • Best For: User-friendly analysis pipelines without requiring coding skills.
5.2. Snakemake

Repository: Snakemake
A flexible pipeline management tool that supports fungal data processing and analysis.

  • Best For: Custom workflows for large-scale fungal datasets.

Conclusion

Fungal research is a rapidly growing field with vast implications for medicine, agriculture, and industry. For bioinformaticians, the availability of specialized resources—databases, tools, and community platforms—opens doors to innovative discoveries. Whether you are investigating fungal genomics, studying host-pathogen interactions, or exploring fungal biodiversity, the resources outlined above will empower your research journey.

Dive into these resources and help unravel the mysteries of the fungal kingdom!

]]> Neel https://bioinformaticsonline.com/blog/view/42974/list-of-bioinformatics-packages-for-ngs-analysis Sat, 20 Mar 2021 00:28:51 -0500 https://bioinformaticsonline.com/blog/view/42974/list-of-bioinformatics-packages-for-ngs-analysis <![CDATA[List of bioinformatics packages for NGS analysis !]]> Package suites gather software packages and installation tools for specific languages or platforms. We have some for bioinformatics software.

  • Bioconductor – A plethora of tools for analysis and comprehension of high-throughput genomic data, including 1500+ software packages. [ paper-2004 | web ]
  • Biopython – Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the Open Bioinformatics Foundation. Contains the very useful Entrez package for API access to the NCBI databases. [ paper-2009 | web ]
  • Bioconda – A channel for the conda package manager specializing in bioinformatics software. Includes a repository with 3000+ ready-to-install (with conda install) bioinformatics packages. [ paper-2018 | web ]
  • BioJulia – Bioinformatics and computational biology infastructure for the Julia programming language. [ web ]
  • Rust-Bio – Rust implementations of algorithms and data structures useful for bioinformatics. [ paper-2016 ]
  • SeqAn – The modern C++ library for sequence analysis.
]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/35057/ectools-long-read-correction-and-other-correction-tools Fri, 05 Jan 2018 04:02:22 -0600 https://bioinformaticsonline.com/bookmarks/view/35057/ectools-long-read-correction-and-other-correction-tools <![CDATA[ECTOOLS: Long Read Correction and other Correction tools]]> Long Read Correction and other Correction tools

This package is a loose collection of scripts. To run the correction
routine see the section below. Descriptions of the other scripts
are at the bottom of this file.

Contact: gurtowsk@cshl.edu

In short, the correction algorithm takes as input the unitigs from a short read assembly and uses them to correct long read data. More background information for the algorithm can be found:
http://schatzlab.cshl.edu/presentations/2013-06-18.PBUserMeeting.pdf

Address of the bookmark: https://github.com/jgurtowski/ectools

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36583/eugi-a-novel-resource-for-studying-genomic-islands-to-facilitate-horizontal-gene-transfer-detection-in-eukaryotes Sat, 12 May 2018 07:26:59 -0500 https://bioinformaticsonline.com/bookmarks/view/36583/eugi-a-novel-resource-for-studying-genomic-islands-to-facilitate-horizontal-gene-transfer-detection-in-eukaryotes <![CDATA[EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer detection in eukaryotes]]> SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in eukaryotes.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4724-8

Address of the bookmark: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4724-8

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/38743/molinspiration-broad-range-of-cheminformatics-software-tools-supporting-molecule-manipulation Sun, 20 Jan 2019 05:32:40 -0600 https://bioinformaticsonline.com/bookmarks/view/38743/molinspiration-broad-range-of-cheminformatics-software-tools-supporting-molecule-manipulation <![CDATA[molinspiration: broad range of cheminformatics software tools supporting molecule manipulation]]> Molinspiration offers broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation, calculation of various molecular properties needed in QSAR, molecular modelling and drug design, high quality molecule depiction, molecular database tools supporting substructure and similarity searches. Our products support also fragment-based virtual screening, bioactivity prediction and data visualization. Molinspiration tools are written in Java, therefore can be used practically on any computer platform.

Address of the bookmark: https://www.molinspiration.com/

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/41996/wgd%E2%80%94simple-command-line-tools-for-the-analysis-of-ancient-whole-genome-duplications Thu, 23 Jul 2020 05:49:45 -0500 https://bioinformaticsonline.com/bookmarks/view/41996/wgd%E2%80%94simple-command-line-tools-for-the-analysis-of-ancient-whole-genome-duplications <![CDATA[wgd—simple command line tools for the analysis of ancient whole-genome duplications]]> wgd is a easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.

https://academic.oup.com/bioinformatics/article/35/12/2153/5162749

Address of the bookmark: https://github.com/arzwa/wgd

]]> LEGE https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly Tue, 17 Aug 2021 13:17:09 -0500 https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly <![CDATA[Bioinformatics tools for telomere to telomere assembly !]]> ● Merfin – k-mer-based assembly and variant calling evaluation for improved consensus accuracy (Arang Rhie)
● PanGenie – algorithm that leverages a pangenome reference built from haplotype-resolved genome assemblies in conjunction with k-mer count information from raw, short-read sequencing data to genotype a wide spectrum of genetic variation (Tobias Marschall)
● SQANTI3 – an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline (Rocío Amorín de Hegedüs @rocioadh)
● tama (Transcriptome Annotation by Modular Algorithms) – software designed for processing Iso-Seq data and other long-read transcriptome data (Richard Kuo @GenomeRIK)
● pbaa (PacBio Amplicon Analysis) – separates complex mixtures of amplicon targets from genomic samples to cluster and generate high-quality consensus sequences from HiFi reads (Zev Kronenberg @zevkronenberg)
● bellerophon – analyzes MHC typing and other low-complexity gene amplicon data; performs allele calling while detecting polymorphic sites within the sequences and removing potential chimeric sequence variants (Yuanyuan Cheng @Yuanyuan929)
● svpack – tools for filtering, comparing, and annotating structural variant (SV) calls in VCF format (Aaron Wenger)
● JumboDB – tool for de Bruijn graph construction (Anton Bankevich @AntonBankevich)
● uLTRA – tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations. (Kristoffer Sahlin @krsahlin)
● LeafGo – workflow to rapidly produce high-quality de novo plant genomes (Luca Ermini @ermini_luca)

Reference:

https://www.pacb.com/blog/young-investigators-share-stellar-science-career-advice-and-bioinformatics-tools-at-smrt-leiden-2021/

 

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools Thu, 17 Feb 2022 05:37:55 -0600 https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools <![CDATA[Comparative genomics visualisation tools !]]> Comparative genomics visualisation tools !

Address of the bookmark: https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&selected=%23BRIG&tag=Comparative

]]> Neel https://bioinformaticsonline.com/blog/view/44551/bioinformatic-tools-for-pathogens-informatics-at-cvr Sat, 08 Jun 2024 15:59:46 -0500 https://bioinformaticsonline.com/blog/view/44551/bioinformatic-tools-for-pathogens-informatics-at-cvr <![CDATA[Bioinformatic tools for pathogens informatics at CVR]]>

Novel sequencing and analytical approaches focused on studying viruses and virus-host interactions. Below you will find summaries and links to a number of bioinformatic tools that have been developed @ CVR.

The database-integrated genome-screening (DIGS) tool provides a framework for implementing automated in silico screening of sequence databases using BLAST in combination with a relational database (MySQL).

DisCVR is a Diagnostic tool for detecting known human viruses in clinical samples from Next-Generation Sequencing (NGS) data. The tool uses a simple and straightforward Graphical User Interface and is optimized on Windows OS without compromising speed and accuracy.

DiversiTools is a computational tool that is specifically tailored towards viral HTS data sets and the analysis of the underlying viral populations that they represent. It was initially developed in collaboration with a number of virologists interested in characterising the intra-host diversity of viral populations and studying their evolution across transmission chains at the micro-evolutionary scale.

GLUE is a flexible data-centric bioinformatics environment for virus sequence data, with a focus on virus evolution and genomic variation. GLUE has been applied to a range of viruses. A GLUE-based resource focused on Hepatitis C virus is HCV-GLUE.

Tanoti is a BLAST guided reference based short read aligner. It is developed for maximising alignment in highly variable next generation sequence data sets (Illumina).

ViCTree is a bioinformatic framework that automatically selects new candidate virus sequences from GenBank, generates multiple sequence alignments, calculates a maximum likelihood phylogeny and integrates the sequences into the existing phylogenetic trees. For more information click here.

Viral Host Predictor provides a fast and simple way to predict the hosts and vectors of RNA viruses from viral sequences.

GRACy is a bioinformatic tool designed for the analysis of Illumina data originated from Human cytomegalovirus samples. GRACy can be used to perform read quality filtering, genotyping, de novo assembly, variant detection, annotation and data submission to public database.

LoReTTA (Long Read Template Targeted Assembler) is a reference assisted de novo assembler specifically designed to deal with PacBio reads generated from viral genomes. 

BingleSeq is a R-package enables the user-friendly analysis of count tables obtained by both Bulk RNA-Seq and single-cell RNA-Seq protocols. The development of BingleSeq focused on providing a flexible and intuitive user experience.

]]> Abhi