Index of /download/sequence/C_albicans_SC5314/Assembly22/current

Icon  Name                                                                               Last modified      Size  Description
[PARENTDIR] Parent Directory                                                                                        -   
[DIR] EMBL_format/                                                                       2024-11-18 02:38    -   
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_other_features_genomic.fasta.gz         2024-11-17 07:03  285K  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_orf_trans_all.fasta.gz                  2024-11-17 07:03  4.7M  
[   ] C_albicans_SC5314_A22_current_other_features_genomic.fasta.gz                      2024-11-17 07:03  285K  
[   ] C_albicans_SC5314_A22_current_orf_trans_all.fasta.gz                               2024-11-17 07:03  4.7M  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_other_features_plus_intergenic.fasta.gz 2024-11-17 07:03  799K  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_other_features_no_introns.fasta.gz      2024-11-17 07:03  285K  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_orf_genomic_1000.fasta.gz               2024-11-17 07:03   15M  
[   ] C_albicans_SC5314_A22_current_other_features_plus_intergenic.fasta.gz              2024-11-17 07:03  799K  
[   ] C_albicans_SC5314_A22_current_other_features_no_introns.fasta.gz                   2024-11-17 07:03  285K  
[   ] C_albicans_SC5314_A22_current_orf_genomic_1000.fasta.gz                            2024-11-17 07:03   15M  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_other_features_genomic_1000.fasta.gz    2024-11-17 07:03  833K  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_orf_coding.fasta.gz                     2024-11-17 07:03  6.8M  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_default_protein.fasta.gz                2024-11-17 07:03  1.8M  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_default_genomic.fasta.gz                2024-11-17 07:03  2.7M  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_default_coding.fasta.gz                 2024-11-17 07:03  2.7M  
[   ] C_albicans_SC5314_A22_current_other_features_genomic_1000.fasta.gz                 2024-11-17 07:03  833K  
[   ] C_albicans_SC5314_A22_current_orf_coding.fasta.gz                                  2024-11-17 07:03  6.8M  
[   ] C_albicans_SC5314_A22_current_default_protein.fasta.gz                             2024-11-17 07:03  1.8M  
[   ] C_albicans_SC5314_A22_current_default_genomic.fasta.gz                             2024-11-17 07:03  2.7M  
[   ] C_albicans_SC5314_A22_current_default_coding.fasta.gz                              2024-11-17 07:03  2.7M  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_orf_plus_intergenic.fasta.gz            2024-11-17 07:03   13M  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_orf_genomic.fasta.gz                    2024-11-17 07:03  6.8M  
[   ] C_albicans_SC5314_A22_current_orf_plus_intergenic.fasta.gz                         2024-11-17 07:03   13M  
[   ] C_albicans_SC5314_A22_current_orf_genomic.fasta.gz                                 2024-11-17 07:03  6.8M  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_not_feature.fasta.gz                    2024-11-17 07:01  3.3M  
[   ] C_albicans_SC5314_A22_current_not_feature.fasta.gz                                 2024-11-17 07:01  3.3M  
[   ] C_albicans_SC5314_version_A22-s07-m01-r226_chromosomes.fasta.gz                    2024-11-17 07:01  8.4M  
[   ] C_albicans_SC5314_A22_current_chromosomes.fasta.gz                                 2024-11-17 07:01  8.4M  

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

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

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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