Index of /download/sequence/C_albicans_SC5314/Assembly19/current

Icon  Name                                                                                      Last modified      Size  Description
[PARENTDIR] Parent Directory - [   ] C_albicans_SC5314_version_A19-s01-m04-r05_other_features_plus_intergenic.fasta.gz 2023-06-29 09:53 166K [   ] C_albicans_SC5314_A19_current_other_features_plus_intergenic.fasta.gz 2023-06-29 09:53 166K [   ] C_albicans_SC5314_version_A19-s01-m04-r05_orf_genomic.fasta.gz 2023-06-29 09:53 6.2M [   ] C_albicans_SC5314_A19_current_orf_genomic.fasta.gz 2023-06-29 09:53 6.2M [   ] C_albicans_SC5314_version_A19-s01-m04-r05_not_feature.fasta.gz 2023-06-29 09:53 3.4M [   ] C_albicans_SC5314_A19_current_not_feature.fasta.gz 2023-06-29 09:53 3.4M [   ] C_albicans_SC5314_version_A19-s01-m04-r05_chromosomes.fasta.gz 2023-06-29 09:53 8.1M [   ] C_albicans_SC5314_A19_current_chromosomes.fasta.gz 2023-06-29 09:53 8.1M [   ] C_albicans_SC5314_A19_current_other_features_plus_intergenic_haploid.fasta.gz 2023-06-29 09:53 92K [   ] C_albicans_SC5314_A19_current_other_features_no_introns_haploid.fasta.gz 2023-06-29 09:53 9.3K [   ] C_albicans_SC5314_version_A19-s01-m04-r05_other_features_genomic_1000.fasta.gz 2023-06-29 09:53 192K [   ] C_albicans_SC5314_version_A19-s01-m04-r05_orf_plus_intergenic.fasta.gz 2023-06-29 09:53 13M [   ] C_albicans_SC5314_A19_current_other_features_genomic_1000.fasta.gz 2023-06-29 09:53 192K [   ] C_albicans_SC5314_A19_current_orf_plus_intergenic.fasta.gz 2023-06-29 09:53 13M [   ] C_albicans_SC5314_version_A19-s01-m04-r05_orf_genomic_1000.fasta.gz 2023-06-29 09:53 13M [   ] C_albicans_SC5314_version_A19-s01-m04-r03_other_features_genomic_1000_haploid.fasta.gz 2023-06-29 09:53 110K [   ] C_albicans_SC5314_A19_current_other_features_genomic_1000_haploid.fasta.gz 2023-06-29 09:53 110K [   ] C_albicans_SC5314_A19_current_orf_genomic_1000.fasta.gz 2023-06-29 09:53 13M [   ] C_albicans_SC5314_version_A19-s01-m04-r05_orf_coding.fasta.gz 2023-06-29 09:53 6.2M [   ] C_albicans_SC5314_A19_current_orf_coding.fasta.gz 2023-06-29 09:53 6.2M [   ] C_albicans_SC5314_A19_current_orf_plus_intergenic_haploid.fasta.gz 2023-06-29 09:53 7.1M [   ] C_albicans_SC5314_version_A19-s01-m04-r05_orf_trans_all.fasta.gz 2023-06-29 09:53 4.2M [   ] C_albicans_SC5314_A19_current_orf_trans_all.fasta.gz 2023-06-29 09:53 4.2M [   ] C_albicans_SC5314_version_A19-s01-m04-r03_orf_trans_all_haploid.fasta.gz 2023-06-29 09:53 2.4M [   ] C_albicans_SC5314_version_A19-s01-m04-r03_orf_genomic_haploid.fasta.gz 2023-06-29 09:53 3.4M [   ] C_albicans_SC5314_A19_current_orf_genomic_1000_haploid.fasta.gz 2023-06-29 09:53 7.3M [   ] C_albicans_SC5314_version_A19-s01-m04-r03_other_features_genomic_haploid.fasta.gz 2023-06-29 09:53 9.8K [   ] C_albicans_SC5314_version_A19-s01-m04-r03_orf_coding_haploid.fasta.gz 2023-06-29 09:53 3.4M [   ] C_albicans_SC5314_version_A19-s01-m04-r03_orf_genomic_1000_haploid.fasta.gz 2023-06-29 09:53 7.3M [   ] C_albicans_SC5314_version_A19-s01-m04-r05_other_features_no_introns.fasta.gz 2023-06-29 09:53 13K [   ] C_albicans_SC5314_version_A19-s01-m04-r05_other_features_genomic.fasta.gz 2023-06-29 09:53 14K [   ] C_albicans_SC5314_A19_current_other_features_no_introns.fasta.gz 2023-06-29 09:53 13K [   ] C_albicans_SC5314_A19_current_other_features_genomic_haploid.fasta.gz 2023-06-29 09:53 9.8K [   ] C_albicans_SC5314_A19_current_other_features_genomic.fasta.gz 2023-06-29 09:53 14K [   ] C_albicans_SC5314_A19_current_orf_coding_haploid.fasta.gz 2023-06-29 09:53 3.4M [   ] C_albicans_SC5314_version_A19-s01-m04-r03_other_features_no_introns_haploid.fasta.gz 2023-06-29 09:53 9.3K [   ] C_albicans_SC5314_A19_current_orf_trans_all_haploid.fasta.gz 2023-06-29 09:53 2.4M [   ] C_albicans_SC5314_version_A19-s01-m04-r03_other_features_plus_intergenic_haploid.fasta.gz 2023-06-29 09:53 92K [   ] C_albicans_SC5314_A19_current_orf_genomic_haploid.fasta.gz 2023-06-29 09:53 3.4M [   ] C_albicans_SC5314_version_A19-s01-m04-r03_orf_plus_intergenic_haploid.fasta.gz 2023-06-29 09:53 7.1M [   ] Ca19-supercontigs-haploid.fasta.gz 2023-06-29 09:53 4.4M [   ] Ca19-supercontigs.fasta.gz 2023-06-29 09:53 7.8M [   ] Ca19-mtDNA.fasta.gz 2023-06-29 09:53 12K
This directory contains the most up-to-date version of the genomic sequences
for Candida albicans SC5314, Assembly 19 (A19).

Assembly 19 is now considered to be archival, and files are not regularly updated.
The gene model and sequence updates described in Butler et al. (2009) were
made only in Assembly 21 (not Assembly 19), and the incremental sequence or
gene model annotation updates that are part of our curation process are
only made in the current assembly (Assembly 21, as of August 2010), not in the
archival assemblies (including Assembly 19). The primary exceptions are updates
to features on the mitochondrial contig (see below) and corrections of major
annotation errors that are discovered in Assembly 19.  All the updates we have
made subsequent to the divergence of Assemblies 19 and 21 are detailed here:
http://www.candidagenome.org/cgi-bin/genomeVersionHistory.pl?seq_source=C.%20albicans%20SC5314%20Assembly%2019

At this time, the current mitochondrial sequence and annotation is
shared between Assembly 19 and Assembly 21. Because the Assembly 21
dataset contained no mitochondrial sequence as it was released by the
BRI, the mitochondrial reference that we include as part of the
current Assembly 21 reference set is technically part of Assembly 19.
Thus, when we update mitochondrial features the genome versions of
both Assemblies 19 and 21 are incremented.

The notation "version_A19-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

Sequence 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 sequence files.

These files are updated occasionally, as described above:

* Sequence with no introns for all ORFs:
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_orf_coding.fasta.gz
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_orf_coding_haploid.fasta.gz
   
* Sequence with introns for all ORFs:
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_orf_genomic.fasta.gz
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_orf_genomic_haploid.fasta.gz

* Sequence with introns for all ORFs, plus flanking 1000 bp upstream and downstream:
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_orf_genomic_1000.fasta.gz
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_orf_genomic_1000_haploid.fasta.gz

* Sequences with introns for all ORFs, plus upstream and downstream intergenic sequence:
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_orf_plus_intergenic.fasta.gz  
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_orf_plus_intergenic_haploid.fasta.gz  

* Translation of all ORFs:
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_orf_trans_all.fasta.gz
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_orf_trans_all_haploid.fasta.gz

* Sequence of non-ORF features (tRNA, rRNA, repeat regions, etc.) with any introns removed:
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_other_features_no_introns.fasta.gz
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_other_features_no_introns_haploid.fasta.gz

* Sequence of non-ORF features including introns:
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_other_features_genomic.fasta.gz
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_other_features_genomic_haploid.fasta.gz

* Sequence of non-ORF features including introns and flanking 1000 bp upstream and downstream:
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_other_features_genomic_1000.fasta.gz
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_other_features_genomic_1000_haploid.fasta.gz

* Sequence of non-ORF features including introns and upstream and downstream intergenic sequence:
	        C_albicans_SC5314_version_A19_sXX-mYY-rZZ_other_features_plus_intergenic.fasta.gz 
	        C_albicans_SC5314_version_A19_sXX-mYY-rZZ_other_features_plus_intergenic_haploid.fasta.gz 

* Sequence between annotated chromosomal features:
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_not_features.fasta.gz
                C_albicans_SC5314_version_A19_sXX-mYY-rZZ_not_features_haploid.fasta.gz
        Note: this file contains genomic DNA sequences between (and excluding) the
        following feature types:
                Protein Coding Sequence
                tRNA
                rRNA
                other non-coding RNAs
                repeat regions
                ARS
                centromere
                telomere
                transposable elements

These files are not updated:

* Sequence of Assembly 19 contigs, supercontigs and mitochondrial DNA:           
	Ca19-mtDNA.fasta.gz
		This file contains the mitochondrial DNA sequence.
	Ca19-supercontigs-haploid.fasta.gz
		This file contains the sequences for the haploid set of Assembly 19 supercontigs in FASTA format.
	Ca19-supercontigs.fasta.gz
		This file contains the sequences for the diploid set of Assembly 19 supercontigs in FASTA format. 

#################################################################################

The files in this directory are in FASTA format.

All files are gzip compressed. There are several freely available
software options for decompressing gzipped files.  The software 
and other useful information is available on these web sites:
- WinZip (http://www.winzip.com/)
- Stuffit (http://www.stuffit.com/)
- Gzip (http://www.gzip.org/

and the gzip user's manual:
http://www.math.utah.edu/docs/info/gzip_toc.html

Additional sequence documentation is found on the CGD web site at:
http://www.candidagenome.org/help/SequenceHelp.shtml

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