bioinformatics
Projects with this topic
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Lectures by Sven Rahmann in the form of Jupyter notebooks
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auxiliary tools for bioinformatic pipelines and sequencing data manipulation
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Fungal Secreted Proteins (or Secretome) Predictor Pipeline
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Fungal Secreted Proteins (or Secretome) Annotation Pipeline
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[mirror] BAM file annotation with mutations.
This is just a mirror. Head over to Codeberg.org for active development
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Snakemake RNAseq processing pipeline (STAR or Salmon) via a SLURM cluster
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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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CommunityYeastract database and web php front-end
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DuploMap is designed to improve precision and recall of long-read alignments in segmental duplications.
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Environment-dependent evolution of digital organisms simulator.
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Alignment search tool that identifies similar proteomes
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A tree-based orthology inference program with additional functionality for reducing contamination.
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A Swiss Knife suite to manage pipeline environments
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Run Oxford Nanopore MinION software in Docker containers
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Master thesis - Deep learning-based pairwise alignment of protein sequences using transformer architecture.
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Python scripting for molecular dynamics simulation using GROMACS
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