bioinformatics
Projects with this topic
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Scripts for pathway enumeration and random flux sampling of metabolite exchanges in microbial models.
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Master thesis - Deep learning-based pairwise alignment of protein sequences using transformer architecture.
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Bioinformatics - Pairwise sequence alignment using hidden Markov model.
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Alignment search tool that identifies similar proteomes
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Manikineko PYBIDK An Python Toolkit for Handling Gentic Information
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DuploMap is designed to improve precision and recall of long-read alignments in segmental duplications.
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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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Snakemake RNAseq processing pipeline (STAR or Salmon) via a SLURM cluster
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Custom scripts or projects.
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Package for the building of Protein-Protein/DNA Complexes in Python
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Bioinformatics toolkit, written in Python and PyQT with Rust plugin system.
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