What's New?
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:
- 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.
- Untranslated regions (5' and 3') were added to over 1900 genes based on available EST data, and 20 alternatively spliced transcripts were manually annotated.
- tRNA and rRNA features have been assigned NCU numbers and, where possible, provided with names from the compendium.
- A mitochondrial annotation from Dr. Richard Collins is available for download and also for BLASTing.
- 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:
Marker Contig Linkage Group nit-2 7.59 I nuo21.3c 7.4 VI Tel-VR 7.37 V
Assembly Data
February 17, 2005
We are pleased to announce release 7 of the Neurospora crassa genome and annotations. Release 7 is based on the finishing work represented in release 6 and contains 850 Kb of additional sequence.
It also includes a putative gene set created using the same tools and methods as the release 3 annotation, but incorporating additional EST data and an updated set of Genbank proteins. The additional sequence and available evidence has allowed us to identify 682 new genes and refine the structures of many others.
A complete description of the creation of the gene set is available.
Release 7 contains 850K of sequence not in release 6. This sequence was present in release 3 but has only recently come out of the finishing process.
- 39 Mb total length of combined contigs (39,225,835 bp)
- Contigs 6.1 to 6.141 correspond to contigs 7.1 to 7.141
- Contigs 7.142 to 7.251 contain added sequence
- Contig 6.15 (778,129 bases) was extended with new sequence to a total length of 817,408 bases.
March 13, 2004
Release 6 represents the improved quality of the genome sequence resulting from ongoing laboratory and computer finishing work.
The goal of our finishing work has been to manually review and edit all sequence to achieve a uniform quality standard across the entire sequence and to close sequence gaps, those gaps that are spanned by one of our many different subclone types (either plasmid, cosmid, Fosmid, or BAC). In Release 6 all but 37 of the original 674 sequence gaps have been closed and, with the exception of a few regions containing ambiguous bases, the entire sequence has been brought to "finished" standards. Those gaps to do remain are represented by a sequence of 50 N's in the contigs.
- Greater than 10X sequencing coverage of the genome
- 141 contigs of finished quality
- 156.2 kb average contig length