Abstract:

This dataset consists primarily of bioinformatic scripts written in python for processing comparative genomics projects along with a readme file with script usage examples. The dataset also includes excel files with the information on the genome accessions and taxonomy for sequences used for reference, 16S RNA statistics, the ratio of shared genes for bacterial comparison, Basic Local Alignment Search Tool (BLAST) results, and details of significantly shared and unshared Gene Ontology (GO) terms for bacterial genomes. This dataset supports the publication: Sevigny, J. L., Rothenheber, D., Diaz, K. S., Zhang, Y., Agustsson, K., Bergeron, R. D., & Thomas, W. K. (2019). Marker genes as predictors of shared genomic function. BMC Genomics, 20(1). doi:10.1186/s12864-019-5641-1.

Suggested Citation:

Joseph L. Sevigny, Derek Rothenheber, Krystalle Sharlyn Diaz, Ying Zhang, Kristin Agustsson, R. Daniel Bergeron, W. Kelley Thomas. 2019. Dataset for: Marker genes as predictors of shared genomic function. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-tc8j-1562

Publications:

Sevigny, J. L., Rothenheber, D., Diaz, K. S., Zhang, Y., Agustsson, K., Bergeron, R. D., & Thomas, W. K. (2019). Marker genes as predictors of shared genomic function. BMC Genomics, 20(1). doi:10.1186/s12864-019-5641-1

Purpose:

The purpose of this data is to assist in the conclusions drawn from metabarcoding studies.

Data Parameters and Units:

Genome Accession, Amount, Score (optional), kingdom, phylum, class, order, family, genus, species, genome, copy_number, min_len, max_len, len_avg, min_%, max_%, number members with same copy number and % variation, Dataset, Percent_ID, Percent_Shared_Genes, Two genome compared, Percent Orthology, Blast query, Blast Subject, Number of Unassigned Genes, Unassigned Genes Matched at 95%, Unassigned Genes Matched at 70%, Ontology, GO.ID, Term, Count-shared, Count-unshared, P-value.

Individual Files: