Index of /download/sequence/A_nidulans_FGSC_A4/current

Icon  Name                                                                           Last modified      Size  Description
[DIR] Parent Directory - [   ] A_nidulans_FGSC_A4_current_chromosomes.fasta.gz 30-Nov-2017 13:43 8.9M [   ] A_nidulans_FGSC_A4_current_not_feature.fasta.gz 30-Nov-2017 13:43 3.9M [   ] A_nidulans_FGSC_A4_current_orf_coding.fasta.gz 30-Nov-2017 13:46 5.7M [   ] A_nidulans_FGSC_A4_current_orf_genomic.fasta.gz 30-Nov-2017 13:46 6.3M [   ] A_nidulans_FGSC_A4_current_orf_genomic_1000.fasta.gz 30-Nov-2017 13:46 13M [   ] A_nidulans_FGSC_A4_current_orf_plus_intergenic.fasta.gz 30-Nov-2017 13:46 50M [   ] A_nidulans_FGSC_A4_current_orf_trans_all.fasta.gz 30-Nov-2017 13:46 3.9M [   ] A_nidulans_FGSC_A4_current_other_features_genomic.fasta.gz 30-Nov-2017 13:46 12K [   ] A_nidulans_FGSC_A4_current_other_features_genomic_1000.fasta.gz 30-Nov-2017 13:46 148K [   ] A_nidulans_FGSC_A4_current_other_features_no_introns.fasta.gz 30-Nov-2017 13:46 11K [   ] A_nidulans_FGSC_A4_current_other_features_plus_intergenic.fasta.gz 30-Nov-2017 13:46 137K [   ] A_nidulans_FGSC_A4_unmapped_Broad_CDS.fasta.gz 24-Feb-2011 10:11 26K [   ] A_nidulans_FGSC_A4_version_s10-m04-r06_chromosomes.fasta.gz 30-Nov-2017 13:43 8.9M [   ] A_nidulans_FGSC_A4_version_s10-m04-r06_not_feature.fasta.gz 30-Nov-2017 13:43 3.9M [   ] A_nidulans_FGSC_A4_version_s10-m04-r06_orf_coding.fasta.gz 30-Nov-2017 13:46 5.7M [   ] A_nidulans_FGSC_A4_version_s10-m04-r06_orf_genomic.fasta.gz 30-Nov-2017 13:46 6.3M [   ] A_nidulans_FGSC_A4_version_s10-m04-r06_orf_genomic_1000.fasta.gz 30-Nov-2017 13:46 13M [   ] A_nidulans_FGSC_A4_version_s10-m04-r06_orf_plus_intergenic.fasta.gz 30-Nov-2017 13:46 50M [   ] A_nidulans_FGSC_A4_version_s10-m04-r06_orf_trans_all.fasta.gz 30-Nov-2017 13:46 3.9M [   ] A_nidulans_FGSC_A4_version_s10-m04-r06_other_features_genomic.fasta.gz 30-Nov-2017 13:46 12K [   ] A_nidulans_FGSC_A4_version_s10-m04-r06_other_features_genomic_1000.fasta.gz 30-Nov-2017 13:46 148K [   ] A_nidulans_FGSC_A4_version_s10-m04-r06_other_features_no_introns.fasta.gz 30-Nov-2017 13:46 11K [   ] A_nidulans_FGSC_A4_version_s10-m04-r06_other_features_plus_intergenic.fasta.gz 30-Nov-2017 13:46 137K [DIR] EMBL_format/ 11-Dec-2017 02:31 -
This directory contains the most current version of Aspergillus nidulans FGSC A4
genomic sequences.

PLEASE NOTE: The sequence file names, as well as the chromosome identifiers within
the files, were updated in July and August 2010 to include the name of the species
and strain. This change was necessary to accommodate multiple Aspergillus and
Aspergillus-related species and strains at AspGD.

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. nidulans FGSC A4 can be found at:
http://www.aspergillusgenome.org/cgi-bin/genomeVersionHistory.pl?seq_source=A.%20nidulans%20FGSC%20A4

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 sequence:
                A_nidulans_FGSC_A4_version_sXX-mYY-rZZ_chromosomes.fasta.gz   

* Sequence with no introns for all ORFs:
                A_nidulans_FGSC_A4_version_sXX-mYY-rZZ_orf_coding.fasta.gz         

* Sequence with introns for all ORFs:
                A_nidulans_FGSC_A4_version_sXX-mYY-rZZ_orf_genomic.fasta.gz 
                
* Sequence with introns for all ORFs, plus flanking 1000 bp upstream and downstream:
                A_nidulans_FGSC_A4_version_sXX-mYY-rZZ_orf_genomic_1000.fasta.gz  

* Sequences with introns for all ORFs, plus upstream and downstream intergenic sequence:
	        A_nidulans_FGSC_A4_version_sXX-mYY-rZZ_orf_plus_intergenic.fasta.gz  

* Translation of all ORFs:
                A_nidulans_FGSC_A4_version_sXX-mYY-rZZ_orf_trans_all.fasta.gz

* Sequence of non-ORF features (tRNA, rRNA, repeat regions, etc.) with any introns removed:
                A_nidulans_FGSC_A4_version_sXX-mYY-rZZ_other_features_no_introns.fasta.gz

* Sequence of non-ORF features including introns:
                A_nidulans_FGSC_A4_version_sXX-mYY-rZZ_other_features_genomic.fasta.gz

* Sequence of non-ORF features including introns and flanking 1000 bp upstream and downstream:
                A_nidulans_FGSC_A4_version_sXX-mYY-rZZ_other_features_genomic_1000.fasta.gz

* Sequence of non-ORF features including introns and upstream and downstream intergenic sequence:
	        A_nidulans_FGSC_A4_version_sXX-mYY-rZZ_other_features_plus_intergenic.fasta.gz  

* Sequence between annotated chromosomal features:
                A_nidulans_FGSC_A4_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

The following file is not updated:

* Coding sequence (no introns) from the Broad annotation updates (2009):
                A_nidulans_FGSC_A4_unmapped_Broad_CDS.fasta.gz

        Note: This file contains new genes in the Broad Institute (2009)
        annotation set that were un-mappable to the Version 4 chromosomal
        sequence, and consequently were not assigned chromosomal coordinates
        or sequence in the initial release of the Version 5 annotation.
        The sequence in this file is based on the Version 3 contigs. This
        file does not contain the coding sequence for gene models from the
        Broad annotation that were intended to be updated versions of existing
        genes. These modifications were rejected from inclusion in the Version 5
        reference annotation because the gene could not be mapped completely to
        the Version 4 chromosomal sequence.  (We can provide these sequences
        upon request.) The processing of the Broad updates and generation of
        Version 5 of the annotation is described in more detail in the AspGD
        Sequence Documentation:

        http://www.aspgd.org/help/SequenceHelp.shtml#Anids_assemblies.

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

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.  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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