This directory contains the downloadable CGD GFF files. These files describe features in CGD, including chromosomes, Contig19s, ORFs, tRNAs, centromeres, sequence gaps, etc. Please see http://song.sourceforge.net/gff3.shtml for a detailed description of the Generic Feature Format (GFF). The file candida_21.gff contains the current CGD annotation based on Assembly 21 of the C. albicans genome sequence. It is updated weekly. The file candida_20.gff contains the current CGD annotation based on Assembly 20 of the C. albicans genome sequence. It is updated weekly. The file suspect_WO1_regions_reduced.gff contains all of the regions that were flagged by the BRI as potentially derived from strain WO-1, rather than the reference strain, SC5314. CGD compared the 1kb flanking parts of each suspect region to Contig19 sequences and iteratively reduced the flanking region from the gap end by 100 bp (10%) until either there was 100% identity with the contig, or 100% could not be found. Thus, the section of the flanking region which aligns perfectly with the contig has been removed from the suspect list. These are the regions that appear with the label "Suspect WO1" in the Genome Browser on the CGD web site. Please see http://www.candidagenome.org/help/Assembly20_Advisory.shtml for additional details. The file candida_19.gff contains CGD annotation from Assembly 19 of the C. albicans genome sequence. This file is a snapshot of current annotation as of September 2006, immediately before the data from Assembly 20 was loaded into CGD. This file is archival; it will not be updated. The file Assem19mapping.gff contains mappings of historic assemblies to Assembly 19 super contigs. BLAST analysis was performed to map Contigs and ORF sequences from each of the older assemblies to the Assembly 19 supercontigs. Please see http://candidagenome.org/download/mapping_historic_assemblies/ for further details on the analysis procedure and separate mapping files for individual assemblies. The file Assem20mapping.gff contains mappings of historic assemblies to Assembly 20 chromosomes. BLAST analysis was performed to map Contigs and ORF sequences from each of the older assemblies to the Assembly 20 chromsomes. Please see http://candidagenome.org/download/mapping_historic_assemblies/ for further details on the analysis procedure and separate mapping files for individual assemblies. The file Assem21mapping.gff contains mappings of historic assemblies to Assembly 21 chromosomes. BLAST analysis was performed to map Contigs and ORF sequences from each of the older assemblies to the Assembly 21 chromsomes. Please see http://candidagenome.org/download/mapping_historic_assemblies/ for further details on the analysis procedure and separate mapping files for individual assemblies. The file A19_ForcheSNPs.gff contains all the SNP locations from Forche A, Magee PT, Magee BB, May G Genome-wide single-nucleotide polymorphism map for Candida albicans. Eukaryotic Cell. 2004 Jun;3(3):705-14. SNP locations were mapped to Assembly 19 contigs using the original marker sequences. The file A20_ForcheSNPs.gff contains all the SNP locations from Forche A, Magee PT, Magee BB, May G Genome-wide single-nucleotide polymorphism map for Candida albicans. Eukaryotic Cell. 2004 Jun;3(3):705-14. SNP locations were mapped to Assembly 20 chromosomes using the original marker sequences. The file A21_ForcheSNPs.gff contains all the SNP locations from Forche A, Magee PT, Magee BB, May G Genome-wide single-nucleotide polymorphism map for Candida albicans. Eukaryotic Cell. 2004 Jun;3(3):705-14. SNP locations were mapped to Assembly 21 chromosomes using the original marker sequences. The file A21_gaps_Nruns.gff lists stretches of continuous unknown bases, denoted as N, that are 3 or more bases long anywhere on A21 chromosomes. The file 5prime_utr_intron_A20.gff or 5prime_utr_intron_A21.gff contains the 5' UTR intron data published in the paper Mitrovich QM, Tuch BB, Guthrie C, Johnson AD. Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans. Genome Res. 2007 Apr;17(4):492-502. These introns are mapped to Assembly 20 or Assembly 21, respectively.