coordinatestosequence
coordinatestosequence extracts nucleotide sequences (DNA or RNA) from user-specified genomic coordinates for downstream genomic, metagenomic, and phylogenetic analyses.
Key Features:
- Sequence Extraction: Retrieves precise DNA or RNA sequences corresponding to user-defined genomic coordinates.
- Galaxy Integration: Executes sequence retrieval within the Galaxy@Pasteur environment using Galaxy's execution framework.
- API Interoperability: Communicates programmatically with Galaxy via its API or the Bioblend library.
Scientific Applications:
- Metagenomics: Enables extraction of specific regions from complex metagenomic assemblies for targeted analyses.
- Phylogenetics: Provides precise sequence retrieval needed for alignment and evolutionary tree construction.
- General Genomic Research: Supports diverse genomic studies that require accurate subsequence data for downstream analyses.
Methodology:
Uses Galaxy as the execution engine on the Institut Pasteur cluster and communicates with Galaxy through its API or via the Bioblend library.
Topics
Collections
Details
- Maturity:
- Mature
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 12/19/2016
- Last Updated:
- 6/16/2020
Operations
Data Inputs & Outputs
Formatting
Publications
Mareuil F, Doppelt-Azeroual O, Ménager H. A public Galaxy platform at Pasteur used as an execution engine for web services. Unknown Journal. 2017. doi:10.7490/f1000research.1114334.1.
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research. 2016;44(W1):W3-W10. doi:10.1093/nar/gkw343. PMID:27137889. PMCID:PMC4987906.