universal_grass_peps

Mitchell, Rowan

(2023) universal_grass_peps. [Data Collection]

Copy

This dataset is the output from a bioinformatics pipeline developed by Rowan Mitchell during 2018-2024 that seeks to identify all universal protein-coding genes in grasses and to estimate how specific they are to grasses. The dataset has 5 components: (1) universal_grass_peps.xlsx contains summary information on all the universal groups of peps identified. (2) files in genBlastG/* are genome annotation files for each novel gene model generated by the genBlastG files in the pipeline. (3) hmms/*.msa.fa are the multiple alignment sequence fasta files, one for each group. (4) files hmms/final_db.hmms* are for use to search the database with query sequences using the HMMER package. (5) files in lookup/* allow users to find which groups a grass query pep ID is a member of, or associated to, for 16 different grass species.

Item Type	Data Collection
Creators	Mitchell, Rowan
Keywords	genomic features; data analysis; networks
Project	Xylan arabinosyl transferases: identification and characterisation of their role in determining properties of grass cell walls, Designing Future Wheat (DFW) [ISPG]
Date	5 December 2023
Data collection method	The genomic sequences that were used in the pipeline were taken from Ensembl Plants release 56 (February 2023). https://feb2023-plants.ensembl.org/index.html
Publisher	Rothamsted Research
Digital Object Identifier (DOI)	10.23637/rothamsted.98ywz