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The pan-genome of Saccharomyces cerevisiae - MaRDI portal

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The pan-genome of Saccharomyces cerevisiae

From MaRDI portal



DOI10.5281/zenodo.3407352Zenodo3407352MaRDI QIDQ6719885

Dataset published at Zenodo repository.

Author name not available (Why is that?)

Publication date: 13 March 2019

Copyright license: No records found.



Description

Thesedatasets are related to The pan-genome of Saccharomyces cerevisiae (Li G., Ji B., and Nielsen J.). This deposition contains following datasets: (1) Genomes.tar.gz: a compressed file containing 1392 Saccharomyces cerevisiaegenome assembles analyzed (2) genome_information_2.0.tsv: a tab-separated text file that contains the basic information of above genomes, including genomeSize, contigNums, N50, busco_C(%), busco_S(%), busco_D(%), busco_F(%), busco_M(%), busco_n, number_of_genes, number_of_partial_genes, download_from, Eco_Source, Ploidy, Aneuploidies. (3) ClusterFasta.tar.gz: a compressed file that contains a list of fasta files. Each fasta file contains protein sequences in a cluster. The name of the fasta file is the name of the representative sequence of that cluster. (4) sc_gene_cluster_info_0.7_v4.tsv: a tab-separated text file that contains the properties of gene clusters. (5)gene_presence_absence_v4.tsv: a tab-separated text file that contains the gene-presence/absence information. Each columns is a gene cluster. Each row is a genome. Y/Nis used to present presence/absence. (6)gene_num_in_clusters_of_each_strain_v4.tsv: a tab-sparated text file that contains the gene number of each genome in each cluster (copy number).Each columns is a gene cluster. Each row is a genome. (7)feature_importances_cv5_pa_cnv.tsv: a tab-separated file that contains the feature importance from a random forest classifier in a 5-fold cross-validation approach. The classifier was trained on gene presence/absence table (PA) or copy number table (CNV). The columns pa_x indicate the feature importance in each fold of cross-validation on PA dataset.The columns cnv_x indicate the feature importance in each fold of cross-validation on CNVdataset.






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