Index of /download/gff/C_albicans_SC5314/Assembly19

Icon  Name                                                                                Last modified      Size  Description
[PARENTDIR] Parent Directory                                                                                         -   
[   ] A19_ForcheSNPs.gff                                                                  2023-06-29 09:53   82K  
[   ] Assem19mapping.gff                                                                  2023-06-29 09:53  1.8M  
[TXT] C_albicans_SC5314_A19_current_intergenic.gff                                        2023-06-29 09:53  2.1M  
[TXT] C_albicans_SC5314_version_A19-s01-m04-r05_intergenic.gff                            2023-06-29 09:53  2.1M  
[TXT] C_albicans_SC5314_A19_current_features.gff                                          2023-06-29 09:53   10M  
[TXT] C_albicans_SC5314_version_A19-s01-m04-r05_features.gff                              2023-06-29 09:53   10M  
[   ] C_albicans_SC5314_A19_current_features.gtf                                          2023-06-29 09:53  3.4M  
[   ] C_albicans_SC5314_version_A19-s01-m04-r05_features.gtf                              2023-06-29 09:53  3.4M  
[   ] C_albicans_SC5314_A19_current_features_with_chromosome_sequences.gff.gz             2023-06-29 09:53  9.3M  
[   ] C_albicans_SC5314_version_A19-s01-m04-r05_features_with_chromosome_sequences.gff.gz 2023-06-29 09:53  9.3M  

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_A19_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 19 can be found at:
http://www.candidagenome.org/cgi-bin/genomeVersionHistory.pl?seq_source=C.%20albicans%20SC5314%20Assembly%2019

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 19 files are updated only when major changes to the underlying
sequence or gene models are incorporated.  For a record of the changes made
to Assembly 19 subsequent to the divergence of Assemblies 19 and 21, see:
http://www.candidagenome.org/cgi-bin/genomeVersionHistory.pl?seq_source=C.%20albicans%20SC5314%20Assembly%2019

C_albicans_SC5314_version_A19-sXX-mYY-rZZ_features.gff
    This file contains CGD annotation from Assembly 19 of the C. albicans
    genome sequence. It is primarily archival and is rarely updated.  It
    was converted to the canonical GFF3 format in October 2012.

C_albicans_SC5314_version_A19-sXX-mYY-rZZ_features.gtf
    This file contains the most recent CGD annotation of protein-coding genes in GTF
    based on Assembly 19 of the C. albicans SC5314 genome sequence.

C_albicans_SC5314_version_A19-sXX-mYY-rZZ_features_with_chromosome_sequences.gff.gz
    This file contains CGD annotation from Assembly 19 of the C. albicans genome
    sequence and the genomic sequence of all the contigs based on Assembly 19.
    The annotations in this file and the previous file are the same.  The contig
    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).

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.

Assem19mapping.gff
    This file contains mappings of historic assemblies to Assembly 19 supercontigs.
    BLAST analysis was performed to map Contigs and ORF sequences from each of the
    older assemblies to the Assembly 19 supercontigs.  For further details on the
    analysis procedure and separate mapping files for individual assemblies, please
    see http://candidagenome.org/download/mapping_historic_assemblies/

A19_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.