inst/extdata/yeast_genome/README.md

In jvanheld/stats4bioinfo: Utilities for the book "Statistics for bioinformatics"

File content

yeast_cds_2001.tab

Coordinates of coding sequences in the genome of the budding yeast (Saccharomyces cerevisiae), from the 2001 annotations. These annotations were essentially done by applying an automatic rule: any ORF of length >= 300 was considered as a putative coding gene.

yeast_cds_2014.tab

Coordinates of coding sequences in the genome of the budding yeast (Saccharomyces cerevisiae), from the 2014 annotations.

These annotations were cleaned with the cumulated results of 18 years of additional research on the yeast genome, including transcriptome analysis and comparative genomics. In particular, ~500 pseudo-ORFs have been removed from the annotations.

yeast_3nt_freq_whole_genome.tab

Trinucleotide frequencies counted in the full genome of the yeast Sacccharomyces cerevisiae, on both strands separately, all occurrences counted (renewing and overlapping).

rand_genome_cds.tab

ORF predictions from a random sequence generated according to a Markov model of order 2, whose parameters were estimated from 3-mer frequencies in the full genome of Saccharomyces cerevisiae.

Note: I temporarily copy twice the results with 8 chromosomes, because the NCBI ORF finder does not accept sequences >1Mb, and I thus have to run it separately for each chromosome. This means that the data is a duplication of an experiment with half the genome size, but since the goal is to estimate ORF length distributions, it should be a reasonable approximation.

jvanheld/stats4bioinfo documentation built on May 20, 2019, 5:16 a.m.