Index of /download/gff/C_albicans_SC5314/Assembly22

Icon  Name                                                                                Last modified      Size  Description
[PARENTDIR] Parent Directory                                                                                         -   
[TXT] C_albicans_SC5314_version_A22-s08-m01-r01_intergenic.gff                            2024-12-08 07:00  2.6M  
[   ] C_albicans_SC5314_version_A22-s08-m01-r01_features_with_chromosome_sequences.gff.gz 2024-12-08 07:00  9.7M  
[   ] C_albicans_SC5314_version_A22-s08-m01-r01_features.gtf                              2024-12-08 07:00  4.2M  
[TXT] C_albicans_SC5314_version_A22-s08-m01-r01_features.gff                              2024-12-08 07:00   13M  
[   ] C_albicans_SC5314_haplotype_variations.gff                                          2023-06-29 09:53   18M  
[TXT] C_albicans_SC5314_A22_current_intergenic.gff                                        2024-12-08 07:00  2.6M  
[   ] C_albicans_SC5314_A22_current_features_with_chromosome_sequences.gff.gz             2024-12-08 07:00  9.7M  
[   ] C_albicans_SC5314_A22_current_features.gtf                                          2024-12-08 07:00  4.2M  
[TXT] C_albicans_SC5314_A22_current_features.gff                                          2024-12-08 07:00   13M  
[   ] A22_Unannotated_transcripts_Tuch_et_al.gff                                          2023-06-29 09:53  534K  
[   ] A22_Unannotated_transcripts_Sellam_et_al.gff                                        2023-06-29 09:53  736K  
[   ] A22_Unannotated_transcripts_Bruno_et_al.gff                                         2023-06-29 09:53  262K  
[TXT] A22_Jones_PMID_15123810_Polymorphisms.vcf                                           2023-06-29 09:53   11M  
[   ] A22_Jones_PMID_15123810_Polymorphisms.gff                                           2023-06-29 09:53   15M  
[   ] A22_Historic_Assemblies.gff                                                         2023-06-29 09:53   14M  
[   ] A22_ForcheSNPs.gff                                                                  2023-06-29 09:53  127K  
[   ] 5prime_utr_intron_A22.gff                                                           2023-06-29 09:53   12K  

This directory contains the downloadable CGD files in the Generic
Feature Format (GFF).  These files describe features in CGD, including 
chromosomes, ORFs, CDSs, introns, sequence gaps, intergenic regions, etc.
We also provide annotation of protein-coding genes in Gene Transfer Format (GTF).

Please see http://www.sequenceontology.org/gff3.shtml for a detailed description 
of the Generic Feature Format (GFF).

Please see http://mblab.wustl.edu/GTF22.html for a description
of the Gene Transfer Format (GTF).

The notation "version_A22_sXX-mYY-rZZ" in the filenames indicates the genome version
to which data in the file corresponds. Detailed explanation about the genome
version notation can be found at: http://www.candidagenome.org/help/SequenceHelp.shtml#versions
Information pertaining to each version update for C. albicans SC5314 Assembly 22 can be found at:
http://www.candidagenome.org/cgi-bin/genomeVersionHistory.pl?seq_source=C.%20albicans%20SC5314%20Assembly%2022

Files with "current" in their names are provided as stable filenames for
automated downloads. They are identical to (technically, symbolic links to) the
corresponding versioned files.

Files for previous genome versions are available in the archive sub-directory,
http://www.candidagenome.org/download/gff/C_albicans_SC5314/archive/.

The following Assembly 22 files are updated weekly:

C_albicans_SC5314_version_A22-sXX-mYY-rZZ_features.gff
    This file contains the current CGD annotation of all features in GFF
    based on Assembly 22 of the C. albicans SC5314 genome sequence.

C_albicans_SC5314_version_A22-sXX-mYY-rZZ_features.gtf
    This file contains the current CGD annotation of protein-coding genes in GTF
    based on Assembly 22 of the C. albicans SC5314 genome sequence.

C_albicans_SC5314_version_A22-sXX-mYY-rZZ_features_with_chromosome_sequences.gff.gz
    This file contains the current CGD annotation and the current genomic sequence
    of all chromosomes of the genome sequence. The annotations in this file and the
    previous file are the same. The chromosome sequences are specified 
    in the "##FASTA" section at the end of this file according to GFF3 file format 
    specifications (see http://www.sequenceontology.org/gff3.shtml).

C_albicans_SC5314_version_A22-sXX-mYY-rZZ_intergenic.gff
    This file lists the intergenic regions between coding regions in the
    chromosomes. This file also contains lengths of these intergenic sequences
    and GC and AT content of each intergenic region (percent GC and percent AT).

The following files map special features or historic assemblies to current assemblies.
The mappings are only updated following major sequence updates to the current assemblies.
These files are not converted to the canonical GFF format due to the historic nature
of the data represented.

5prime_utr_intron_A22.gff
    This file contains annotation of the 5-prime UTR introns described in
    Mitrovich et al. (2007) "Computational and experimental approaches double
    the number of known introns in the pathogenic yeast Candida albicans."
    Genome Res 17:492-502.

A22_ForcheSNPs.gff
    This file 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.

A22_Historic_Assemblies.gff
    This file contains mappings of historic assemblies to Assembly 22 chromosomes.
    BLAST analysis was performed to map Contigs and ORF sequences from each of the
    older assemblies to the Assembly 21 chromsomes, and liftOver was used to map
    to Assembly 22.

A22_Jones_PMID_15123810_Polymorphisms.gff
    This file contains all polymorphisms discussed in Jones et al. (2004) "The Diploid
    Genome of Candida albicans." PNAS 101:7329-7334.  Polymorphism locations were mapped
    to Assembly 21 using 50 bp flanking sequence on both sides of each polymorphism to
    locate exact matches using BLAST.  Locations for "Deletion" type polymorphism indicates
    the region that is deleted, including the start and stop coordinates. Locations for
    "Insertion" type polymorphism indicate that an insertion has been made in the homolog
    sequence immedeatly AFTER the location specified. Locations for "Substitution" type
    polymorphisms indicate the site of a single nucleotide substitution.
    The liftOver tool was used to map this to Assembly 22.

A22_Jones_PMID_15123810_Polymorphisms.vcf
    Same as above, converted to vcf format.

A22_Unannotated_transcripts_Bruno_et_al_2010.gff
    This file contains novel transcriptionally active regions detected in high-throuhgput
    sequencing of cDNA (RNA-seq) under several environmental conditions, described in
    Bruno VM, Wang Z, Marjani SL, Euskirchen GM, Martin J, Sherlock G, Snyder M (2010)
    "Comprehensive annotation of the transcriptome of the human fungal pathogen Candida
    albicans using RNA-seq." Genome Res 20(10):1451-8

A22_Unannotated_transcripts_Sellam_et_al.gff
    This file contains novel, unannotated transcripts detected in tiling microarray experiments
    from Sellam A, Hogues H, Askew C, Tebbji F, van het Hoog M, Lavoie H, Kumamoto CA, Whiteway M,
    Nantel A "Experimental annotation of the human pathogen Candida albicans coding and noncoding  
    transcribed regions using high-resolution tiling arrays." Genome Biol 2010; 11(7):R71.

A22_Unannotated_transcripts_Tuch_et_al_2010.gff
    This file contains novel, unannotated transcriptionally active regions detected by strand-specific
    sequencing of RNA from white and opaque cells, described in Tuch BB, Mitrovich QM, Homann OR,
    Hernday AD, Monighetti CK, De La Vega FM, Johnson AD (2010) "The transcriptomes of two heritable
    cell types illuminate the circuit governing their differentiation." PLoS Genet 6(8)