Saturday, May 25, 2024

BIOINFORMATICS TOOLS

Gene Prediction

  • GENEID – A program to predict genes, exons, splice sites and other signals along a DNA sequence.
  • AUGUSTUS – Program that predicts genes in eukaryotic genomic sequences.
  • EuGene – Integrative gene finder for eukaryotic and prokaryotic genomes.
  • PseudoPipe – A stand alone computational pipeline for pseudogene annotation.
  • GenScan – Web server for the identification of complete gene structures in genomic DNA.
  • HMMgene – 1.1 – Program for prediction of vertebrate and C. elegans genes.

Must Read

Can We Truly Understand Proteins Through Text? ProtT3 Says Yes!

Can We Truly Understand Proteins Through Text? ProtT3 Says Yes!

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The discovery of ProtT3 marks a significant recent advance in the fast-developing science of bioinformatics. ProtT3, developed by researchers at the National University of...
Decoding VEXAS Syndrome: How Single-Cell Genotype-Phenotype Mapping Identifies New Treatment Avenues

Decoding VEXAS Syndrome: How Single-Cell Genotype-Phenotype Mapping Identifies New Treatment Avenues

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Clonal variation emerges across tissues as a result of somatic evolution, with far-reaching consequences for human health. The VEXAS (Vacuoles E1 enzyme X-linked Autoinflammatory...
StarFunc: Revolutionizing Protein Function Prediction Leveraging Template-based and Deep Learning Approaches

StarFunc: Revolutionizing Protein Function Prediction Leveraging Template-based and Deep Learning Approaches

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A recent study by the Chengxin Zhang lab from the University of Michigan introduced StarFunc, an accurate protein function prediction approach integrating cutting-edge deep...
Decoding Protein Function with ProteinCLIP: How Natural Language Enhances Protein Language Models

Decoding Protein Function with ProteinCLIP: How Natural Language Enhances Protein Language Models

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Language models have made a new era of biological sequence modeling possible. However, it is still difficult to extract significant sequence-level embeddings from these...
SYNY: A Powerful Pipeline for Investigating and Visualizing Genome Collinearity

SYNY: A Powerful Pipeline for Investigating and Visualizing Genome Collinearity

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Scientists have questioned the comparison of genes' organization across various species. Collinearity analysis is a helpful way to go about this task, although it...