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DIYA: a bacterial annotation pipeline for any genomics lab
By Jit 2701 days agosourceforge.net - DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and...chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
By Neel 2050 days agocran.r-project.org - Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special...Web Apollo: a web-based genomic annotation editing platform
By Jit 2673 days agogenomearchitect.github.io - Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new...bpRNA: large-scale automated annotation and analysis of RNA secondary structure
By Rahul Nayak 2374 days agogithub.com - bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with...KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH...
By Abhimanyu Singh 2171 days agowww.kegg.jp - KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data...Apollo: First instantaneous, collaborative genomic annotation editor available on the Web
By Jit 2001 days agogenomearchitect.github.io - Apollo is a plug-in for the JBrowse Genome Viewer. In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own...JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
By Jit 1710 days agogithub.com - Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. https://github.com/tanghaibao/jcvi More at https://github.com/tanghaibao/jcvi/wikiMetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic...
By Jit 1408 days agogithub.com - MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. Metaeuk combines the fast and sensitive homology search capabilities of MMseqs2 with a dynamic programming procedure to...CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
By Shruti Paniwala 911 days agogitlab.com - CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of other tools in order to get an improved precision and recall. Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It...SIMON BOULTON LAB
DNA is quite fragile and easily damaged, both by the normal processes of life at work within our cells and by external agents such as the chemicals in tobacco smoke or ultraviolet (UV) rays from the sun. However, our cells have evolved clever...
