Index of /download/sequence/C_albicans_SC5314/Assembly19/current
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Ca19-supercontigs.fasta.gz 2023-06-29 09:53 7.8M
Ca19-supercontigs-haploid.fasta.gz 2023-06-29 09:53 4.4M
Ca19-mtDNA.fasta.gz 2023-06-29 09:53 12K
C_albicans_SC5314_version_A19-s01-m04-r05_other_features_plus_intergenic.fasta.gz 2023-06-29 09:53 166K
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_1000.fasta.gz 2023-06-29 09:53 192K
C_albicans_SC5314_version_A19-s01-m04-r05_other_features_genomic.fasta.gz 2023-06-29 09:53 14K
C_albicans_SC5314_version_A19-s01-m04-r05_orf_trans_all.fasta.gz 2023-06-29 09:53 4.2M
C_albicans_SC5314_version_A19-s01-m04-r05_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-r05_orf_genomic.fasta.gz 2023-06-29 09:53 6.2M
C_albicans_SC5314_version_A19-s01-m04-r05_orf_coding.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_version_A19-s01-m04-r05_chromosomes.fasta.gz 2023-06-29 09:53 8.1M
C_albicans_SC5314_version_A19-s01-m04-r03_other_features_plus_intergenic_haploid.fasta.gz 2023-06-29 09:53 92K
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_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_other_features_genomic_1000_haploid.fasta.gz 2023-06-29 09:53 110K
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_plus_intergenic_haploid.fasta.gz 2023-06-29 09:53 7.1M
C_albicans_SC5314_version_A19-s01-m04-r03_orf_genomic_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-r03_orf_coding_haploid.fasta.gz 2023-06-29 09:53 3.4M
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_plus_intergenic.fasta.gz 2023-06-29 09:53 166K
C_albicans_SC5314_A19_current_other_features_no_introns_haploid.fasta.gz 2023-06-29 09:53 9.3K
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_1000_haploid.fasta.gz 2023-06-29 09:53 110K
C_albicans_SC5314_A19_current_other_features_genomic_1000.fasta.gz 2023-06-29 09:53 192K
C_albicans_SC5314_A19_current_other_features_genomic.fasta.gz 2023-06-29 09:53 14K
C_albicans_SC5314_A19_current_orf_trans_all_haploid.fasta.gz 2023-06-29 09:53 2.4M
C_albicans_SC5314_A19_current_orf_trans_all.fasta.gz 2023-06-29 09:53 4.2M
C_albicans_SC5314_A19_current_orf_plus_intergenic_haploid.fasta.gz 2023-06-29 09:53 7.1M
C_albicans_SC5314_A19_current_orf_plus_intergenic.fasta.gz 2023-06-29 09:53 13M
C_albicans_SC5314_A19_current_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_A19_current_orf_genomic_1000.fasta.gz 2023-06-29 09:53 13M
C_albicans_SC5314_A19_current_orf_genomic.fasta.gz 2023-06-29 09:53 6.2M
C_albicans_SC5314_A19_current_orf_coding_haploid.fasta.gz 2023-06-29 09:53 3.4M
C_albicans_SC5314_A19_current_orf_coding.fasta.gz 2023-06-29 09:53 6.2M
C_albicans_SC5314_A19_current_not_feature.fasta.gz 2023-06-29 09:53 3.4M
C_albicans_SC5314_A19_current_chromosomes.fasta.gz 2023-06-29 09:53 8.1M
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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