Index of /download/sequence/A_oryzae_RIB40/current

Icon  Name                                                                       Last modified      Size  Description
[DIR] Parent Directory                                                                                -   
[   ] A_oryzae_RIB40_version_s01-m05-r06_chromosomes.fasta.gz                    13-May-2012 08:02   11M  
[   ] A_oryzae_RIB40_version_s01-m05-r06_not_feature.fasta.gz                    13-May-2012 10:09  5.6M  
[   ] A_oryzae_RIB40_version_s01-m05-r06_orf_coding.fasta.gz                     13-May-2012 09:26  5.7M  
[   ] A_oryzae_RIB40_version_s01-m05-r06_orf_genomic.fasta.gz                    13-May-2012 08:25  6.5M  
[   ] A_oryzae_RIB40_version_s01-m05-r06_orf_genomic_1000.fasta.gz               13-May-2012 08:15   14M  
[   ] A_oryzae_RIB40_version_s01-m05-r06_orf_plus_intergenic.fasta.gz            13-May-2012 08:59   18M  
[   ] A_oryzae_RIB40_version_s01-m05-r06_orf_trans_all.fasta.gz                  13-May-2012 09:50  4.0M  
[   ] A_oryzae_RIB40_version_s01-m05-r06_other_features_genomic.fasta.gz         13-May-2012 09:51   14K  
[   ] A_oryzae_RIB40_version_s01-m05-r06_other_features_genomic_1000.fasta.gz    13-May-2012 09:50  186K  
[   ] A_oryzae_RIB40_version_s01-m05-r06_other_features_no_introns.fasta.gz      13-May-2012 09:52   13K  
[   ] A_oryzae_RIB40_version_s01-m05-r06_other_features_plus_intergenic.fasta.gz 13-May-2012 09:51  230K  
[DIR] EMBL_format/                                                               17-May-2012 13:33    -   

This directory contains the most current version of Aspergillus oryzae RIB40
genomic sequences.

The notation "sXX-mYY-rZZ" in the filename indicates the genome version to which data in 
the file corresponds. Detailed explanation about the genome version can 
be found at: http://www.aspgd.org/help/SequenceHelp.shtml#Anids_versions 

These files are updated weekly:

* Chromosomal sequence:
                A_oryzae_RIB40_version_sXX-mYY-rZZ_chromosomes.fasta.gz   

* Sequence with no introns for all ORFs:             
                A_oryzae_RIB40_version_sXX-mYY-rZZ_orf_coding.fasta.gz         

* Sequence with introns for all ORFs:
                A_oryzae_RIB40_version_sXX-mYY-rZZ_orf_genomic.fasta.gz 
                
* Sequence with introns and untranslated region 1000 bp upstream and
downstream for all ORFs:
                A_oryzae_RIB40_version_sXX-mYY-rZZ_orf_genomic_1000.fasta.gz  

* Sequences with introns plus upstream and downstream intergenic
sequence for all ORFs:
	        A_oryzae_RIB40_version_sXX-mYY-rZZ_orf_plus_intergenic.fasta.gz  

* Translation of all ORFs:
                A_oryzae_RIB40_version_sXX-mYY-rZZ_orf_trans_all.fasta.gz

* Sequence of tRNAs (predicted using tRNAscan-SE), includes sequence of any introns:
                A_oryzae_RIB40_version_sXX-mYY-rZZ_other_features_genomic.fasta.gz
Note: sequence of other non-ORF feature types will be added to this file when these 
features are added to AspGD in the future.

* Genomic sequence of tRNAs (predicted using tRNAscan-SE), plus region 
1000 bp upstream and downstream:
                A_oryzae_RIB40_version_sXX-mYY-rZZ_other_features_genomic_1000.fasta.gz
Note: sequence of other non-ORF feature types will be added to this file when these 
features are added to AspGD in the future.

* Genomic sequence of tRNAs (predicted by tRNAscan-SE) plus upstream and downstream intergenic
sequence:
	        A_oryzae_RIB40_version_sXX-mYY-rZZ_other_features_plus_intergenic.fasta.gz  
Note: sequence of other non-ORF feature types will be added to this file when these 
features are added to AspGD in the future.

* Sequence of tRNAs (predicted using tRNAscan-SE), with introns removed:
                A_oryzae_RIB40_version_sXX-mYY-rZZ_other_features_no_introns.fasta.gz
Note: sequence of other non-ORF feature types will be added to this file when these 
features are added to AspGD in the future.


* Sequence between annotated chromosomal features (see note below):
                A_oryzae_RIB40_version_sXX-mYY-rZZ_not_feature.fasta.gz  
Note: this file contains DNA sequences which are between chromosomal features.
Features excluded from this file are ARS, ORF, centromere, long_terminal_repeat, 
ncRNA, pseudogene, rRNA, retrotransposon, snRNA, snoRNA, tRNA, telomere, 
telomeric_repeat, transposable_element_gene, blocked_reading_frame, repeat_region.
The file is in compressed FASTA format.  This file is updated whenever features 
are added or removed or there are changes to feature boundaries.
The archive/ directory lists all the A_oryzae_RIB40_version_sXX-mYY-rZZ_not_feature.fasta.gz 
files from the past.


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The files in this directory are in FASTA format.

The FASTA header lines include the AN and ANID identifier for each 
ORF, the contig number (Version 3), the contig coordinates, the strand, 
a brief description from the Broad, and the length of the sequence 
in nucleotides.

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 AspGD web site at:
http://www.aspergillusgenome.org/help/SequenceHelp.shtml

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