Index of /download/sequence/Assembly21

 Name                    Last modified      Size  Description
 Parent Directory                             -   
 archive/                13-May-2008 01:30    -   
 archived_as_released/   03-Dec-2007 17:33    -   
 current/                13-May-2008 01:32    -   

The /download/sequence/ directory contains sequence from the
C. albicans genome sequencing project, and derivatives thereof.

Current files are generated weekly and reflect the most current
information at CGD.  Most of the files in this directory are in FASTA
format; current Assembly 20 and Assembly 21 files in EMBL format may
be downloaded from the /Assembly20/current/EMBL_format/ and
/Assembly21/current/EMBL_format/ subdirectories, respectively.

All files are gzip compressed. There are several freely available
software options for decompressing gzipped files using Windows.  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

------------------------------------------------

/Assembly21/

This directory contains sequence files for Assembly 21


/Assembly21/current/        

This directory contains the most current version of the sequences;
files are updated weekly:

sequence with introns for all ORFs:
	orf_genomic_assembly_21.fasta.gz

sequence with no introns for all ORFs:
	orf_coding_assembly_21.fasta.gz

sequences with introns and untranslated region 1000 bp upstream and
downstream for all ORFs:
	orf_genomic_1000_assembly_21.fasta.gz  

translation of all ORF regions:
	orf_trans_all_assembly_21.fasta.gz 


sequences from the systematic C. albicans sequence for the following
feature types: ARS, CEN, rRNA, tRNA, snRNA, snoRNA, ncRNA genes 
(other types will be added in future):
	other_features_genomic_assembly_21.fasta.gz 
	other_features_no_introns_assembly_21.fasta.gz 

genomic sequence for the above features plus 1000 bp upstream and
downstream sequence:
	other_features_genomic_1000_assembly_21.fasta.gz 


/Assembly21/current/EMBL_format/

This directory contains current gene and sequence data from the
C. albicans Assembly 21 genome in EMBL file format.  Files in this
directory are generated weekly and reflect the most current
information at CGD.

/Assembly21/archived_as_released/
                
This directory contains Candida albicans Assembly 21 (A21), as
released to CGD by the A21 collaborators and described in van Het Hoog
et al., 2007: http://genomebiology.com/content/pdf/gb-2007-8-4-r52.pdf

Please note that the sequence files have not been subject to analyses
at CGD.

		Ca21Chr1.zip
                Ca21Chr2.zip
                Ca21Chr3.zip
                Ca21Chr4.zip
                Ca21Chr5.zip
                Ass20+OG0611.seq
                Chromosome 7v04_4.seq 
                Ca21ChrR.zip

The .zip archives containing Chromosomes 1 through 5 and R were
submitted to CGD by Marco van Het Hoog; these files are the output of
"Sequencher" software.  Ass20+OG0611.seq and Chromosome 7v04_4.seq
contain Chromosome 6 and Chromosome 7, respectively, and these files
were submitted to CGD by Hiroji Chibana.

                 All_Ca21_chromosomes.fa.gz

The A21 sequences have been extracted from each of the archives, and
collected in a single multi-fasta file (All_Ca21_chromosomes.seq.gz)
for easy downloading and use.



/Assembly21/archive/

This directory contains archived versions of the Assembly 19
sequences.  The sequences are checked for changes weekly and a new
file is added whenever there has been a change.  The date of the
update is included in the filename.