S288c Genome Chip

 

gff files

 

General Feature Format annotation files

Specifications for the file format can be found at The Sanger Institute and UCSC's Genome Browser pages. One of the imput file types used by IGB and other genome browsers.

 

File name
(downloadable, larger files are zipped)
Description
Version1 zip archive of 17 individual gff files. Annotation with coordinates relative to sequence used to tile chip. Not all chromosomes were released to GenBank before further updates, so gff files for these were created by hand editing GenBank records.
ver1_allinOne Single file with containing all 16 chromosomes + mitochondria. Annotation with coordinates relative to sequence used to tile chip. Not all chromosomes were released to GenBank before further updates, so gff files for these were created by hand editing GenBank records.
2005Jan_sgdCDS_RNA Version current as of Jan. 2005. Annotation is directly from SGD rather then GenBank. Contains data from 16 chromosomes + mitochondria. SGD provides several useful classifications not easily parsed from GenBank, such as dubious ORFs.
Custom gff files
UniqYJM A "faux" chromosome has been constructed that puts together all the unique YJM789 sequence. More details are on the Unique YJM789 page.
Arabidopsis controls there are several Arabidopsis mRNA (cDNA) sequences tiled in single bp tiles on the chip. This file is used with a fasta file that lets one view all of data for these probes at one time in IGB
Duplicated Probes locations in S288c genome of probes on chip that are present more then once in genome