News

1/15/2010    SNP Identification for current release of C. albicans SC5314

We have repeated the SNP detection process for the current release of C. albicans SC5314 (Release Date: 25-Nov-2008). SNPs were discovered by comparing the sequence reads of WO-1 and SC5314 with the above reference assembly using the Neighborhood Quality Standard (NQS) algorithm.

SNP data can be downloaded here.

3/24/2009    SNP Identification

We have identified single nucleotide polymorphisms for two C. albicans, C. tropicalis, L. elongisporus and C. parapsilosis strains.

SNPs were discovered by comparing the sequencing reads with the reference assembly.

The reads were aligned with the assembly using the Blat algorithm. The alignments thus obtained were filtered; reads that did not have a unique placement in the assembly or had >20% gaps in them were rejected.

Neighborhood Quality Standard (NQS) algorithm was used to identify high confidence polymorphic sites. SNPs were identified as single-base sequence variants that had a minimum PHRED base quality of 25 at the position of mismatch, a neighborhood base quality of 20, and no mismatches within 5 bp.

SNP data can be downloaded here

1/26/2009    Annotation of Ribosomal RNA Genes

We have added the fully annotated ribosomal RNA genes for C. albicans WO1, C. guilliermondii, C. lusitaniae, C. tropicalis and L. elongisporus. In addition, the ribosomal RNA genes for the updated C. parapsilosis can be downloaded here. The ribosomal rRNA genes were identified using a combination of RNAmmer and RFAM.

4/14/2007    Links to CGD and CandidaDB

We have added links from each gene page to the corresponding gene pages in CGD (for C. albicans SC5314) and to CandidaDB (for C. albicans (both strains), C. tropicalis, L. elongisporus, C. guilliermondii, C. lusitaniae, and D. hansenii. These are found under "external links" on each gene page.

10/25/2007    Candida Comparative Website release

Release of Candida comparative website including all the Candida related genomes sequenced at the Broad as well as C. albicans SC5314 (Assembly 20), C. dubliniensis (Sanger), and D. hansenii (Genolevures).

10/04/2006    C. albicans WO-1 automated annotation release

A description of the gene-calling method can be found here. This annotated release presents:

  • A predicted protein gene set (6,160 genes)
  • Protein BLAST databases
  • Precomputed results of BlastX and HMMer Analyses
  • tRNA predictions
  • Search and visualizations for all the features

6/12/2006    C. tropicalis automated annotation

A description of the gene-calling method can be found here. This annotated release presents:

  • A predicted protein gene set (6,258 genes)
  • Protein BLAST databases
  • Precomputed results of BlastX and HMMer Analyses
  • tRNA predictions
  • Search and visualizations for all the features

3/15/2006    10X C. albicans WO-1 assembly release

The initial release of our 10X sequence assembly of the Candida albicans WO-1 assembly. The sequence traces from the Broad Institute sequencing can be downloaded from the NCBI trace repository. This Whole Genome Shotgun sequence assembly has been deposited at DDBJ/EMBL/GenBank under the project accession AAFO00000000. The version described in this release is the first version, AAFO01000000.

3/15/2006    C. guilliermondii automated annotation release

Release of the initial results of automated annotation. A description of the gene-calling method can be found here. This annotated release presents:

  • A predicted protein gene set (5,920 genes)
  • Protein BLAST databases
  • Precomputed results of BlastX and HMMer Analyses
  • tRNA predictions
  • Search and visualizations for all the features

1/25/2006    C. lusitaniae automated annotation release

A description of the gene-calling method can be found here. This annotated release presents:

  • A predicted protein gene set (5,941 genes)
  • Protein BLAST databases
  • Precomputed results of BlastX and HMMer Analyses
  • tRNA predictions
  • Search and visualizations for all the features

12/28/2004    12x C. guilliermondii assembly release

The sequence traces from the Broad Institute sequencing can be downloaded from the NCBI trace repository.

11/15/2005    C. tropicalis assembly release

As with assembly 1, assembly 3 represents the diploid genome sequence as a single consensus. In comparison to assembly 1, assembly 3 has minimized the amount of haplotype collapsing in regions of high polymorphism. This has resolved many of the problems with gene structures in assembly 1 resulting from merging divergent sequences.

12/28/2004    9x C. lusitaniae assembly released

The sequence traces from the Broad Institute sequencing can be downloaded from the NCBI trace repository.