S. cerevisiae strain RedStar genome sequence.

02/03/2015

This directory contains 6 files describing the genome of S. cerevisiae strain RedStar, 
a widely-used commercial baking strain (Accession: JRIL00000000; ATCC Number: 58532). 

genome fasta file: RedStar_Stanford_2014_JRIL00000000.fsa
nucleic acid coding sequence file: RedStar_JRIL00000000_cds.fsa
protein sequence file:  RedStar_JRIL00000000_pep.fsa
GFF file: RedStar_JRIL00000000.gff
snv variant call format file: RedStar.gatk.vcf.gz
indel variant call format file: RedStar.indel.gatk.vcf.gz

FASTA headers in each of the files include the following pieces of information:

genome fasta file: 
 GenBank GI number
 GenBank accession.version
 species name
 strain name
 scaffold number
 contig length

nucleic acid coding sequence file: 
 ORF name_strain name
 gene name
 feature type
 feature classification (Verified, Uncharacterized, or Dubious)
 feature description

protein sequence file: 
 ORF name_strain name
 gene name
 feature type
 feature classification (Verified, Uncharacterized, or Dubious)
 feature description

Feature definitions (for coding sequences and features in the gff file) were
assigned via homology-based annotation using LASTZ and AUGUSTUS vs. the R64-1
S288C reference sequence in conjuction with ab initio annotation using MAKER 
and BLASTX validation.

Assembly statistics
================================
Fold coverage:	180
Number of scaffolds:	1812
Assembly size:		12003693
Longest scaffold:	319971
Scaffold N50:		98298
Number of ORFs:		5440


Reference for this S. cerevisiae RedStar genome sequence, assembly and annotation:

Song et al., 2014, AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome 
Analysis of Saccharomyces cerevisiae.  PLoS ONE, in press.

Source for S. cerevisiae RedStar: http://lesaffre-yeast.com/

For more information about the S288C Reference Genome:

Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight 
SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato 
SR, Simison M, Cherry JM. 2014. The reference genome sequence of Saccharomyces 
cerevisiae: then and now. 
G3 (Bethesda). 2014 Mar 20;4(3):389-98. doi: 10.1534/g3.113.008995.

To download the S288C Reference Genome sequence and annotation: 
http://www.yeastgenome.org/download-data/sequence