Index of /download/sequence/A_oryzae_RIB40/current

Icon  Name                                                                       Last modified      Size  Description
[DIR] Parent Directory - [   ] A_oryzae_RIB40_current_chromosomes.fasta.gz 02-Feb-2020 07:35 11M [   ] A_oryzae_RIB40_version_s01-m09-r14_chromosomes.fasta.gz 02-Feb-2020 07:35 11M [   ] A_oryzae_RIB40_current_not_feature.fasta.gz 02-Feb-2020 07:35 5.5M [   ] A_oryzae_RIB40_version_s01-m09-r14_not_feature.fasta.gz 02-Feb-2020 07:35 5.5M [   ] A_oryzae_RIB40_current_orf_coding.fasta.gz 02-Feb-2020 07:37 6.2M [   ] A_oryzae_RIB40_current_orf_genomic.fasta.gz 02-Feb-2020 07:37 7.0M [   ] A_oryzae_RIB40_current_orf_genomic_1000.fasta.gz 02-Feb-2020 07:37 15M [   ] A_oryzae_RIB40_current_orf_plus_intergenic.fasta.gz 02-Feb-2020 07:37 18M [   ] A_oryzae_RIB40_current_orf_trans_all.fasta.gz 02-Feb-2020 07:37 4.2M [   ] A_oryzae_RIB40_current_other_features_genomic.fasta.gz 02-Feb-2020 07:37 14K [   ] A_oryzae_RIB40_current_other_features_genomic_1000.fasta.gz 02-Feb-2020 07:37 192K [   ] A_oryzae_RIB40_current_other_features_no_introns.fasta.gz 02-Feb-2020 07:37 13K [   ] A_oryzae_RIB40_current_other_features_plus_intergenic.fasta.gz 02-Feb-2020 07:37 218K [   ] A_oryzae_RIB40_version_s01-m09-r14_orf_coding.fasta.gz 02-Feb-2020 07:37 6.2M [   ] A_oryzae_RIB40_version_s01-m09-r14_orf_genomic.fasta.gz 02-Feb-2020 07:37 7.0M [   ] A_oryzae_RIB40_version_s01-m09-r14_orf_genomic_1000.fasta.gz 02-Feb-2020 07:37 15M [   ] A_oryzae_RIB40_version_s01-m09-r14_orf_plus_intergenic.fasta.gz 02-Feb-2020 07:37 18M [   ] A_oryzae_RIB40_version_s01-m09-r14_orf_trans_all.fasta.gz 02-Feb-2020 07:37 4.2M [   ] A_oryzae_RIB40_version_s01-m09-r14_other_features_genomic.fasta.gz 02-Feb-2020 07:37 14K [   ] A_oryzae_RIB40_version_s01-m09-r14_other_features_genomic_1000.fasta.gz 02-Feb-2020 07:37 192K [   ] A_oryzae_RIB40_version_s01-m09-r14_other_features_no_introns.fasta.gz 02-Feb-2020 07:37 13K [   ] A_oryzae_RIB40_version_s01-m09-r14_other_features_plus_intergenic.fasta.gz 02-Feb-2020 07:37 218K [DIR] EMBL_format/ 30-Mar-2020 02:36 -
This directory contains the current version of Aspergillus oryzae RIB40/ATCC 42149
genomic sequences.

Aspergillus oryzae RIB40/ATCC 42149 was originally sequenced by the NITE, AIST, A. oryzae
consortium.  Sequence and annotation were downloaded from the Broad Institute Aspergillus
download page on 23-Feb-2009. Gene models were subsequently refined at AspGD by PASA
alignment of A. oryzae ESTs and RNA-Seq provided by Dr. Kazuhiro and RNA-Seq reads
reported in Wang (2010) PMID:20392818.

The notation "version_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.aspgd.org/help/SequenceHelp.shtml#Anids_versions 
Information pertaining to each version update for A. oryzae RIB40/ATCC 42149 can be found at:
http://www.aspergillusgenome.org/cgi-bin/genomeVersionHistory.pl?seq_source=A.%20oryzae%20RIB40

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 weekly:

* Chromosomal/contig 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 for all ORFs, plus flanking 1000 bp upstream and downstream:
                A_oryzae_RIB40_version_sXX-mYY-rZZ_orf_genomic_1000.fasta.gz  

* Sequences with introns for all ORFs, plus upstream and downstream intergenic sequence:
	        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 non-ORF features (tRNA, rRNA, repeat regions, etc.) with any introns removed:
                A_oryzae_RIB40_version_sXX-mYY-rZZ_other_features_no_introns.fasta.gz

* Sequence of non-ORF features including introns:
                A_oryzae_RIB40_version_sXX-mYY-rZZ_other_features_genomic.fasta.gz

* Sequence of non-ORF features including introns and flanking 1000 bp upstream and downstream:
                A_oryzae_RIB40_version_sXX-mYY-rZZ_other_features_genomic_1000.fasta.gz

* Sequence of non-ORF features including introns and upstream and downstream intergenic sequence:
	        A_oryzae_RIB40_version_sXX-mYY-rZZ_other_features_plus_intergenic.fasta.gz  

* Sequence between annotated chromosomal features:
                A_oryzae_RIB40_version_sXX-mYY-rZZ_not_feature.fasta.gz  
        Note: this file contains genomic DNA sequences between (and excluding) the
        following feature types:
                Protein Coding Sequence
                tRNA
                rRNA
                repeat regions

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

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