News

November 4, 2013    Large insert clones mapped to NC12

The paired end-sequences from BAC (PBELOBAC-KAN) and Cosmid (PLORIST and PMOCOSX) libraries was realigned to NC12 to assist with clone retrieval. End sequences with multiple placements are noted in the file on the download page; these locations should be used with caution.

March 11, 2013    Release of the RNAseq-Based Annotation Update of Neurospora crassa

The Neurospora crassa gene set has been updated with strand-specific RNAseq data (from Broad) and 454 transcript data (from Roche/454). Here is a summary:

New genes added: 5
Genes deleted: 2
Genes merged: 16->8
Genes split: 1->2
CDS change: 1388
UTRs changed: 5693
Unchanged: 2633

This release also corrected the previous NC10 orientation for LGVII, as well as the orientation for contig 304 in LGVI.

This annotation update includes 9,730 protein-coding genes and 212 non-coding RNA genes for the nuclear assembly; and 28 protein-coding genes for the mitochondrial assembly (GenBank accession: KC683708).

This annotated release presents:

A mapping between this latest annotation and the previous one can be found from the Downloads page.

A full summary can be found here.

Jun 25, 2010    Release of the Updated Annotation of our Finished assembly of Neurospora crassa

This annotation update includes 9,733 protein-coding genes and 176 non-coding RNA genes for the nuclear assembly; and 28 protein-coding genes for the mitochondrial assembly.

This annotated release presents:

A mapping between this latest annotation and the previous one can be found here, or from the Downloads page.

A full summary can be found here.

Feb 3, 2010    Release of the Annotation of our Finished assembly of Neurospora crassa

Strain Name Total Genes Accession Submission Date
N. crassa OR74A 9,952 AABX03000000 2/3/2010

This annotated release presents:

Please note that supercontings 10.1 ~ 10.7 correspond to Linkage Groups I ~ VII, while the rest are unmapped scaffolds.

A full summary can be found here.

Sep 2, 2009    The release of our Updated Assembly of Neurospora crassa

Strain Name Coverage Accession Submission Date
N. crassa OR74A Finished AABX03000000 9/2/2009

This release allows:

  • BLAST searches against our genome assemblies
  • Downloads of the consensus sequence and additional files for the genome assembly
  • Search and download a particular region of the genome assembly.

Please note this release does not yet include an updated annotation.

May 7, 2007    Protein-coding gene predictions overlapping ribosomal RNA gene regions flagged

The loci for the following protein-coding gene predictions have been flagged due to the fact that they overlap regions of genome predicted to contain ribosomal RNA genes. They have been flagged as "overlaps ribosomal RNA region" on the Gene Details reports and have been segregated into separate files in the Downloads page and on the BLAST page.
  • NCU09753
  • NCU10637
  • NCU11428
  • NCU11366

August 30, 2006    Release of Version 3 annotation for Assembly 7

We are pleased to announce the release of Version 3 gene predictions for the Neurospora crassa assembly 7. A description of the gene finding process, as well as the correspondence between Version 2 and Version 3 can be found here. Version 3 contains 9,826 genes, 794 fewer than Version 2. Other new features for this release include:
  1. Integration of The Neurospora Compendium entries: entries from the compendium have been incorporated as community annotations. Users can now look up genes using this information on the FindFeatures page.
  2. Untranslated regions (5' and 3') were added to over 1900 genes based on available EST data, and 20 alternatively spliced transcripts were manually annotated.
  3. tRNA and rRNA features have been assigned NCU numbers and, where possible, provided with names from the compendium.
  4. A mitochondrial annotation from Dr. Richard Collins is available for download and also for BLASTing.
  5. Previous annotations and characterizations from the Community Annotation project, along with Phenotype characterizations, have been transfered to this new set.

April 11, 2006   

BLAST search has been enhanced with the following features:
  • You can now enter more than one sequence at a time, separated by FASTA header lines. Each sequence will run as a separate job.
  • In the results display, gene-related hits now show up as links to the appropriate gene. This will facilitate searching for genes using BLAST.
  • Also in the results display, hits to genomic sequence link to the appropriate region. From here you may view a feature map of the region or run the Argo applet.

March 30, 2006   

This revamped Neurospora site has two important new features:
  • Richer text-based searching of features. Genes can now be more easily and efficiently searched by description, symbol, Pfam overlap, blast overlaps, and more. See the Feature Search page or the Help page for details.
  • Community annotation. Neurospora researchers are now able to edit gene data and perform functional annotation. All users of the site may view annotated data.

November 3, 2005   

Optical mapping data has been released for the NC7 sequence assembly. 92% of the sequence is now placed in the genome with known order and orientation, in contrast to 65% before the integration of the optical map. The optical mapping information is available in the downloads section, the genetic maps section, and the Assembly Structure table.

May 4, 2005   

We have recently discovered that the genetic map for N. crassa Release 7 was missing three markers, 'nit-2', 'nuo21.3c', and 'Tel-VR'. The contigs & linkage groups affected are:

MarkerContigLinkage Group
nit-27.59I
nuo21.3c7.4VI
Tel-VR7.37V