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GERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models.
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You can safely remove the following: - `GERONIMO/results` - `GERONIMO/database` - `GERONIMO/taxonomy` - `GERONIMO/temp` - `.create_genome_list.touch` - `list_of_genomes.txt`
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By default, the GERONIMO pipeline conducts high-throughput searches of homology sequences in downloaded genomes utilizing covariance models.
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Research Object Crate for GERONIMO
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date published: 2023-09-08 12:04:04.643799+00:00
description: # GERONIMO ## Introduction GERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models. These models are based on the alignment of sequences and the consensus of secondary structures. The pipeline is built using Snakemake, a workflow management tool that allows for the reproducible execution of analyses on various computational platforms. The idea for developing GERONIMO emerged from a comprehensive search for [telomerase RNA in lower plants] and was subsequently refined through an [expanded search of telomerase RNA across Insecta]. GERONIMO can test hundreds of genomes and ensures the stability and reproducibility of the analyses performed. [telomerase RNA in lower plants]: https://doi.org/10.1093/nar/gkab545 [expanded search of telomerase RNA across Insecta]: https://doi.org/10.1093/nar/gkac1202 ## Scope The GERONIMO tool utilises covariance models (CMs) to conduct homology searches of RNA sequences across a wide range of gene families in a broad evolutionary context. Specifically, it can be utilised to: * Detect RNA sequences that share a common evolutionary ancestor * Identify and align orthologous RNA sequences among closely related species, as well as paralogous sequences within a single species * Identify conserved non-coding RNAs in a genome, and extract upstream genomic regions to characterise potential promoter regions. It is important to note that GERONIMO is a computational tool, and as such, it is intended to be run on a computer with a small amount of data. Appropriate computational infrastructure is necessary for analysing hundreds of genomes. Although GERONIMO was primarily designed for Telomerase RNA identification, its functionality extends to include the detection and alignment of other RNA gene families, including **rRNA**, **tRNA**, **snRNA**, **miRNA**, and **lncRNA**. This can aid in identifying paralogs and orthologs across different species that may carry specific fu…
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GERONIMO
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description: # GERONIMO ## Introduction GERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models. These models are based on the alignment of sequences and the consensus of secondary structures. The pipeline is built using Snakemake, a workflow management tool that allows for the reproducible execution of analyses on various computational platforms. The idea for developing GERONIMO emerged from a comprehensive search for [telomerase RNA in lower plants] and was subsequently refined through an [expanded search of telomerase RNA across Insecta]. GERONIMO can test hundreds of genomes and ensures the stability and reproducibility of the analyses performed. [telomerase RNA in lower plants]: https://doi.org/10.1093/nar/gkab545 [expanded search of telomerase RNA across Insecta]: https://doi.org/10.1093/nar/gkac1202 ## Scope The GERONIMO tool utilises covariance models (CMs) to conduct homology searches of RNA sequences across a wide range of gene families in a broad evolutionary context. Specifically, it can be utilised to: * Detect RNA sequences that share a common evolutionary ancestor * Identify and align orthologous RNA sequences among closely related species, as well as paralogous sequences within a single species * Identify conserved non-coding RNAs in a genome, and extract upstream genomic regions to characterise potential promoter regions. It is important to note that GERONIMO is a computational tool, and as such, it is intended to be run on a computer with a small amount of data. Appropriate computational infrastructure is necessary for analysing hundreds of genomes. Although GERONIMO was primarily designed for Telomerase RNA identification, its functionality extends to include the detection and alignment of other RNA gene families, including **rRNA**, **tRNA**, **snRNA**, **miRNA**, and **lncRNA**. This can aid in identifying paralogs and orthologs across different species that may carry specific fu…
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Rfam database
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norm score: 2.8875379939209727
score: 1.9

Detect RNA sequence
type: Phrase
norm score: 3.6474164133738602
score: 2.4

earth sciences
type: FieldOfResearch
norm score: 100.0
score: 0.9349703192710876

taxonomy
type: Concept
norm score: 3.3444816053511706
score: 4.0

search
type: Lemma
norm score: 6.688417618270798
score: 4.1

name
type: Lemma
norm score: 4.893964110929853
score: 3.0

Agata Kilar
type: Person

Mendel Centre for Plant Genomics and Proteomics
type: Organization
type: Project

sig
has algorithm: RSA
signed by: RoCrateBot