Index of /download/sequence/C_albicans_SC5314/Assembly22/current
Name Last modified Size Description
Parent Directory -
C_albicans_SC5314_A22_current_chromosomes.fasta.gz 2024-10-13 07:01 8.4M
C_albicans_SC5314_A22_current_default_coding.fasta.gz 2024-10-13 07:03 2.7M
C_albicans_SC5314_A22_current_default_genomic.fasta.gz 2024-10-13 07:03 2.7M
C_albicans_SC5314_A22_current_default_protein.fasta.gz 2024-10-13 07:03 1.8M
C_albicans_SC5314_A22_current_not_feature.fasta.gz 2024-10-13 07:01 3.3M
C_albicans_SC5314_A22_current_orf_coding.fasta.gz 2024-10-13 07:03 6.8M
C_albicans_SC5314_A22_current_orf_genomic.fasta.gz 2024-10-13 07:03 6.8M
C_albicans_SC5314_A22_current_orf_genomic_1000.fasta.gz 2024-10-13 07:03 15M
C_albicans_SC5314_A22_current_orf_plus_intergenic.fasta.gz 2024-10-13 07:03 13M
C_albicans_SC5314_A22_current_orf_trans_all.fasta.gz 2024-10-13 07:03 4.7M
C_albicans_SC5314_A22_current_other_features_genomic.fasta.gz 2024-10-13 07:03 285K
C_albicans_SC5314_A22_current_other_features_genomic_1000.fasta.gz 2024-10-13 07:03 833K
C_albicans_SC5314_A22_current_other_features_no_introns.fasta.gz 2024-10-13 07:03 285K
C_albicans_SC5314_A22_current_other_features_plus_intergenic.fasta.gz 2024-10-13 07:03 799K
C_albicans_SC5314_version_A22-s07-m01-r222_chromosomes.fasta.gz 2024-10-13 07:01 8.4M
C_albicans_SC5314_version_A22-s07-m01-r222_default_coding.fasta.gz 2024-10-13 07:03 2.7M
C_albicans_SC5314_version_A22-s07-m01-r222_default_genomic.fasta.gz 2024-10-13 07:03 2.7M
C_albicans_SC5314_version_A22-s07-m01-r222_default_protein.fasta.gz 2024-10-13 07:03 1.8M
C_albicans_SC5314_version_A22-s07-m01-r222_not_feature.fasta.gz 2024-10-13 07:01 3.3M
C_albicans_SC5314_version_A22-s07-m01-r222_orf_coding.fasta.gz 2024-10-13 07:03 6.8M
C_albicans_SC5314_version_A22-s07-m01-r222_orf_genomic.fasta.gz 2024-10-13 07:03 6.8M
C_albicans_SC5314_version_A22-s07-m01-r222_orf_genomic_1000.fasta.gz 2024-10-13 07:03 15M
C_albicans_SC5314_version_A22-s07-m01-r222_orf_plus_intergenic.fasta.gz 2024-10-13 07:03 13M
C_albicans_SC5314_version_A22-s07-m01-r222_orf_trans_all.fasta.gz 2024-10-13 07:03 4.7M
C_albicans_SC5314_version_A22-s07-m01-r222_other_features_genomic.fasta.gz 2024-10-13 07:03 285K
C_albicans_SC5314_version_A22-s07-m01-r222_other_features_genomic_1000.fasta.gz 2024-10-13 07:03 833K
C_albicans_SC5314_version_A22-s07-m01-r222_other_features_no_introns.fasta.gz 2024-10-13 07:03 285K
C_albicans_SC5314_version_A22-s07-m01-r222_other_features_plus_intergenic.fasta.gz 2024-10-13 07:03 799K
EMBL_format/ 2024-10-07 02:37 -
This directory contains the most current version of the genomic sequences for
Candida albicans SC5314, Assembly 22 (A22).
Assembly 22 is a phased, diploid assembly. It is described in Muzzey et al. (2013)
Genome Biology 14(9), p. R97
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
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.
Sequence files with "default" in their names contain a haploid complement of features,
where a single allele represents each pair in the diploid genome. The criteria which
allele is chosen are as follows:
(1) Fewer internal stops
(2) Fewer ambiguous bases (if 1 not applicable)
(3) Longer open reading frame (1 and 2 not applicable)
(4) "A" allele (if 1-3 not applicable)
Sequence files without "default" in their names contain both alleles,
with "A" or "B" suffixes in ther names to indicate Haplotype A or Haplotype B, respectively.
These files are updated weekly:
* Chromosomal/contig sequence:
C_albicans_SC5314_version_A22_sXX-mYY-rZZ_chromosomes.fasta.gz
* Sequence with no introns for all ORFs:
C_albicans_SC5314_version_A22_sXX-mYY-rZZ_orf_coding.fasta.gz
* Sequence with introns for all ORFs:
C_albicans_SC5314_version_A22_sXX-mYY-rZZ_orf_genomic.fasta.gz
* Sequence with introns for all ORFs, plus flanking 1000 bp upstream and downstream:
C_albicans_SC5314_version_A22_sXX-mYY-rZZ_orf_genomic_1000.fasta.gz
* Sequences with introns for all ORFs, plus upstream and downstream intergenic sequence:
C_albicans_SC5314_version_A22_sXX-mYY-rZZ_orf_plus_intergenic.fasta.gz
* Translation of all ORFs:
C_albicans_SC5314_version_A22_sXX-mYY-rZZ_orf_trans_all.fasta.gz
* Sequence of non-ORF features (tRNA, rRNA, repeat regions, etc.) with any introns removed:
C_albicans_SC5314_version_A22_sXX-mYY-rZZ_other_features_no_introns.fasta.gz
* Sequence of non-ORF features including introns:
C_albicans_SC5314_version_A22_sXX-mYY-rZZ_other_features_genomic.fasta.gz
* Sequence of non-ORF features including introns and flanking 1000 bp upstream and downstream:
C_albicans_SC5314_version_A22_sXX-mYY-rZZ_other_features_genomic_1000.fasta.gz
* Sequence of non-ORF features including introns and upstream and downstream intergenic sequence:
C_albicans_SC5314_version_A22_sXX-mYY-rZZ_other_features_plus_intergenic.fasta.gz
* Sequence between annotated chromosomal features:
C_albicans_SC5314_version_A22_sXX-mYY-rZZ_not_features.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
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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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