bioinformatics
Projects with this topic
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OTP, One Touch Pipeline, Documentation at https://one-touch-pipeline.gitlab.io/otp/
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Common Workflow Language - computational workflows
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Unix toolkit for feature analysis of alternative splicing events. Includes basic functions for manipulating tables, extraction of exon and intron-related features, discriminate feature analysis, motif maps for RNA-binding proteins, and more.
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Crawl any filesystem for genome data, providing one-click opening in IGV
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Scripts for pathway enumeration and random flux sampling of metabolite exchanges in microbial models.
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A d3 javascript SVG visualization of alternative splicing of randomly seeded exons from a random genome
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Python scripting for molecular dynamics simulation using GROMACS
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Master thesis - Deep learning-based pairwise alignment of protein sequences using transformer architecture.
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Run Oxford Nanopore MinION software in Docker containers
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A Swiss Knife suite to manage pipeline environments
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A tree-based orthology inference program with additional functionality for reducing contamination.
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Alignment search tool that identifies similar proteomes
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Environment-dependent evolution of digital organisms simulator.
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DuploMap is designed to improve precision and recall of long-read alignments in segmental duplications.
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CommunityYeastract database and web php front-end
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This project includes python scripts with examples used for the below article in GBE. It is also archived on Figshare (https://doi.org/10.6084/m9.figshare.17111693).
Red algal plastids exhibit large genome size variation, especially in the recently described subphylum Proteorhodophytina. By contrast, their mitochondrial genomes remain unexplored. Here, we sequenced, assembled, and analyzed new plastid and mitochondrial genomes of 25 species of red microalgae. We uncovered new cases of genome size expansion in plastids and mitochondria, in both cases associated with group II intron proliferation. The phylogenomic analysis supported that these expansions occurred several times independently. URL: https://doi.org/10.1093/gbe/evac037
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