Neurospora crassa Release 7 Downloads

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Files

Sequence (FASTA) filesSizeDate
neurospora_crassa_7.fasta.gz11.6 MB02/16/2005
Download DNA sequences in gzipped FASTA format.
neurospora_crassa_7_genes.fasta.gz4.5 MB02/28/2005
Download DNA sequences for putative gene set in gzipped FASTA format.
neurospora_crassa_7_proteins.fasta.gz2.9 MB02/28/2005
Download translated amino acid sequences for putative gene set in gzipped FASTA format.
neurospora_3_mitochondria.fasta.gz19.3 KB07/22/2005
Download mitochondria DNA sequence in gzipped FASTA format. File contains a single sequence of 64,840 base pairs.
Supplementary filesSizeDate
neurospora_crassa_7_genes_changelist.csv362.2 KB02/25/2005
Comma-separated file contains list of changes to genes from release 3 to current release. Columns are:
OLD_LOCUSLocus of gene in release 3
NEW_LOCUSLocus of gene in release 7
UPDATE_TYPEType of change, either 'ADD','CHANGE','DELETE','MERGE','SPLIT', or 'UNCHANGED'
UPDATE_DETAILAny specific details on update
neurospora_crassa_7_moved_orfs.txt4.2 KB02/18/2005
This file contains a list of 475 genes with a one to one mapping in the previous release where the release 7 start codon is more than 150 bases upstream of the release 3 start codon, or the release 7 stop codon is more than 150 bases downstream of the release 3 stop codon. It does not include added, merged, split, or deleted genes.
neurospora_crassa_7_homology_150bp_changes.txt1.8 KB03/01/2005
This is a list of 201 locus numbers where a release 7 gene corresponds 1 to 1 with a release 3 gene, the ORF of the release 7 gene has widened by 150bp or more at either the 5' or 3' end, and the release 7 gene call is based on homology to a protein in NR.
neurospora_crassa_7_homology_150bp_from_fgenesh_changes.txt900 bytes03/01/2005
This list of 100 locus numbers is the subset of the 201 genes based on protein homology in release 7 whose corresponding release 3 gene was based on an ab-initio gene call (Fgenesh).
neurospora_crassa_7_genes.csv.gz218.6 KB02/25/2005
Comma-separated file contains list of genes in release 7. Columns are:
LOCUSunique locus identifier, including version
NAMEputative gene name
CONTIGcontig number containing gene
STARTstart position (1-origin)
STOPstop position (1-origin)
LENGTHlength of gene
neurospora_crassa_7_exons.csv.gz471.2 KB03/31/2005
Comma-separated file contains exon positions for putative gene set. All coordinates are relative to the contig sequence, and start from position 1. For all features, start is less than or equal to stop and the direction of the feature is indicated by the strand. Columns:
EXON_STARTStart position of exon
EXON_STOPStop position of exon
EXON_STRANDStrand of exon
FULL_GENE_NAMEFull name of gene containing this exon (including locus)
GENE_STARTStart position of gene
GENE_STOPStop position of gene
GENE_LENGTHLength of gene
GENE_STRANDStrand of gene
CONTIG_NAMEName of contig containing gene
GENE_LOCUSFull gene locus
GENE_LOCUS_BASELocus base
GENE_LOCUS_VERSIONLocus version
GENE_NAMEName of gene
neurospora_crassa_7_contigs.csv3.2 KB02/15/2005
Comma-separated file contains columns (see Contig Numbering for details):
CONTIGcontig number
LENGTHlength (bp)
SUPERCONTIGsupercontig number
neurospora_crassa_7_optical_map_info.txt3.1 KB11/03/2005
Correlations found by optical mapping for supercontigs, linkage groups, and markers.
neurospora_crassa_7_combined_maps.xml113.2 KB03/17/2006
XML representation of integration between optical, physical, and genetic maps.
neurospora_crassa_7_poster.png87.2 KB05/04/2005
Poster of physical & genetic map
Upstream/Downstream regions of autocalled genes. The following gzipped FASTA files contain the genomic sequences found upstream of the start codon, or downstream of the stop codon. The distances availalbe are 300,500, or 1000 bases in either direction. Cases where a gene is located near the end of a contig result in a truncated sequence.SizeDate
neurospora_crassa_gene_upstream_300.fasta.gz1.2 MB07/27/2005
sequences found upstream 300 nucleotides from the start codon.
neurospora_crassa_gene_upstream_500.fasta.gz1.9 MB07/27/2005
sequences found upstream 500 nucleotides from the start codon.
neurospora_crassa_gene_upstream_1000.fasta.gz3.6 MB07/27/2005
sequences found upstream 1000 nucleotides from the start codon.
neurospora_crassa_gene_downstream_300.fasta.gz1.2 MB07/27/2005
sequences found downstream 300 nucleotides from the stop codon.
neurospora_crassa_gene_downstream_500.fasta.gz1.9 MB07/27/2005
sequences found downstream 500 nucleotides from the stop codon.
neurospora_crassa_gene_downstream_1000.fasta.gz3.6 MB07/27/2005
sequences found downstream 1000 nucleotides from the stop codon.
Previous releases
The data from previous releases is available for download below, but is not accessible from other parts of the web site.

  1. Assembly 1 (all files)
    • neurospora_1.fasta.gz (11 MB)
      Download sequence in gzipped FASTA format. File contains 1705 contigs totalling 38,244,162 base pairs.
  2. Assembly 2 (all files)
    • neurospora_2.fasta.gz (12 MB)
      Download sequence in gzipped FASTA format. File contains 985 contigs totalling 37,869,317 base pairs.
  3. Assembly 3 (all files)
    • neurospora_3.fasta.gz (12 MB)
      Download sequence in gzipped FASTA format. File contains 821 contigs totalling 38,044,343 base pairs.

You may also download any of these files via the ftp site: ftp://ftp.broad.mit.edu/pub/annotation/fungi/neurospora_crassa/release7

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