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Mycology Research Resources for Bioinformaticians: Unlocking the Fungal Kingdom

Neel — Fri, 13 Dec 2024 11:21:45 -0600

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!

Update Genome Workbench 2.7.15 released

Surabhi Chaudhary — Wed, 26 Feb 2014 16:12:17 -0600

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.

Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.

Genome Workbench is built on the NCBI C++ ToolKit and uses cross-platform APIs for graphics. It runs on your local machine, and is available for Windows 2000/XP, Linux, MacOS X, and various flavors of Unix.

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. Genome Workbench was developed entirely in-house at NCBI and makes use of the NCBI C++ ToolKit. The C++ ToolKit provides a convenient and flexible cross-platform API for managing system internals, database connections, network sockets, and the NCBI data model. In addition, the C++ ToolKit provides the Object Manager, which abstracts handling of sequences and sequence-related objects.

New Features in Genome Workbench 2.7.15

Multiple Alignment View: implemented adaptive feature display when zooming in
Active Objects Inspector replaces Selection Inspector. New View should offer an improved selection context examination. See Using Active Objects Inspector tutorial for more details.
Binary packages for Linux OpenSUSE 13.1 are now available

Bug Fixes and Improvements in Genome Workbench 2.7.15

Fixed major issue with OpenGL overlay/scrolling. Could cause crashes or view scrolling irregularities
Multiple Pane View: fixed crash on loading BLAST results
Graphical Sequence View: fixed crash on zooming in and out, related to SNP track
Graphical Sequence View: fixed Go To Position dialog to give better diagnostics in case of a user error
Graphical Sequence View: PDF export fixed rendering of Markers with commas in the name
Text View / Flat File: fixed Mac OS rendering issues
Text View / Flat File: performance optimization, extended capabilities of real-time rendering of molecules to tens of thousands
File Import: optimization improvement to speed up load of files containing multiple project items
File Import: remapping stage now shows accession.version and description of molecules, instead of plain GI numbers
Mac OS: improved tooltips for toolbar buttons
Phylogenetic Tree Builder Tool: improved diagnostics of errors
Multiple Alignment View: optimizations to avoid main GUI freezes
Open Dialog: removed duplicate elements in table of genomes (load Genome)
PDF export: fixed issue with XREF table errors
Tree View: fixed issues with showing Force Layout progress on Mac OS
Tree View: PDF export fixed issues for showing labels of collapsed nodes
Tree View: added an option to stop layout
Tree View: broadcasting mechanism fixed not to accumulate selected nodes

Reference:

NCBI news

http://www.ncbi.nlm.nih.gov/tools/gbench/

Biological databases !

BioStar — Wed, 12 Feb 2020 01:16:29 -0600

Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

4DGenome

Jitendra Narayan — Mon, 04 Jul 2016 00:44:55 -0500

Records in 4DGenome are compiled through comprehensive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted interactions in 5 organisms. Experimental data cover both high throughput datasets and individiual focused studies.

All interaction data are freely available in a standardized file format. Records can be queried by genomic regions, gene names, organism, and detection technology.

Address of the bookmark: http://4dgenome.research.chop.edu/

Entrez Direct: E-utilities on the UNIX Command Line

Anjana — Wed, 19 Oct 2016 08:06:24 -0500

Entrez Direct (EDirect) is an advanced method for accessing the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions. Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/books/NBK179288/

Eugene V. Koonin Lab

Tue, 09 Jan 2018 05:01:15 -0600

Interested in understanding the evolution of life. To obtain glimpses of such understanding, we employ existing and new methods of computational biology to perform research in several major areas.

https://www.ncbi.nlm.nih.gov/research/groups/koonin/

Bioinformatics Head (Bioinformatics Manager III), Cancer Genomics Research Laboratory at Frederick National Laboratory

Wed, 18 Aug 2021 00:19:48 -0500

Frederick National Laboratory seeking an enthusiastic, creative, and seasoned bioinformatics professional to join our leadership team and direct the exceptional Bioinformatics Group at the Cancer Genomics Research Laboratory (CGR). CGR has a diverse team of bioinformatics and computational scientists that support all areas of bioinformatics and data analysis (infrastructure, data QC, pipeline development and maintenance, data curation and sharing, methodology development, statistical analyses, machine learning approaches, and scientific interpretation).

More at https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leidosbiomed&id=2040

Anders Krogh Lab

Mon, 30 Sep 2013 19:07:40 -0500

In a lot of my work in bioinformatics, I have been using hidden Markov models (HMMs). As a postdoc with David Haussler at UCSC we developed the so-called profile HMMs (refs). Since then I have applied HMMs to membrane proteins (refs) and gene identification (refs) and have worked on methods for such things as discriminative estimation of HMMs (refs) and alternative decoding algorithms etc. (refs).

Now my main interests are in gene regulation, where we work on promoter analysis; non-coding RNA, where miRNAs and structure prediction are the main areas; and protein structure, where the group is working on methods for structure prediction from sequence. To read more about these topics, please see the research pages.

Lab page @ http://wiki.binf.ku.dk/User:Krogh

Bioinformatics Tutorial !

Neel — Mon, 22 Aug 2022 23:56:22 -0500

This site aims to be a useful resource for bioinformatics beginners. Feel free to jump right in with the section most relevant to you, and if you're not sure, then the place to start is definitely Unix

Address of the bookmark: https://astrobiomike.github.io/

CRCRI Bioinfomatics Walk In on 08.10.2013

Fri, 27 Sep 2013 10:59:53 -0500

Walk-in-Interview for recruitment of one Project Fellow for a period of 10 months purely on temporary basis is proposed to be held at Central Tuber Crops Research Institute, Sreekariyam, Thiruvananthapuram for a KSCSTE funded project entitled “PARTICIPATORY DEVELOPMENT OF A WEB BASED USER FRIENDLY CASSAVA EXPERT SYSTEM”

Salary: Rs. 10,000/- per month.

Age limit: 35 for men and 40 for women & SC/ST.

Qualification: First class in M. Sc (Agriculture)/MCA/M.Sc (IT)/ M. Sc (Computer Application)/M.Sc (Bioinformatics)/M.Sc (Geoinformatics).

Desirable: Two years experience in web design and web programming.

Date & time of interview: 08.10.2013, 10 am

Interested candidates may appear for an interview at this institute along with their application in plain paper containing the following particulars viz. (1) Name (2) Father/Husband/Guardian’s Name (3) date of birth & age as on 01.10.2013 (4) Permanent address (5) Address for communication (6) Email address and Telephone No. with code (7) Qualification (8) National fellowship like ICAR/CSIR/UGC etc. if any (9) Whether SC/ST/OBC (10) Details of experience (Attested copies of degree certificate, proof of age, mark sheets). Original certificates should be produced for verification.

No TA/DA will be admissible to the candidates attending the test. The selected candidate will have to join immediately.

Advertisement: http://www.ctcri.org/careers/mithra_SRF.doc