B-3501A assembly data (FASTA files)

• Genomic sequence
  The B-3501A assembly consists of 70 contigs representing 18.5 Mb. The contigs can be placed into 14 scaffolds representing 14 chromosomes. Chromosome assignments were made based on genetic marker data from Bob Marra, Duke University (soon to be published). Most gaps between contigs are small, a few hundred bases or less. Eleven gaps are very large (20 kb - 60 kb). The large gaps are in highly repetitive regions of the genome. In the scaffolds file, large gaps are represented by 1000 N's and small gaps are 100 N's. The rDNA repeat unit is in chromosome 2 and a couple copies are present in the sequence along with a large gap.
  
  • all scaffolds in one file: cneo040623.scaffs.fa.gz (5.6M file)
    
  • individual scaffold files in download directory.

• Predicted protein sequences
  The gene predictions are based on TWINSCAN predictions, TIGR JEC21 gene predictions, and EST data (from OU and TIGR).
  • predicted protein sequences: cneo040623.cds.pep.gz (2.5M file)
    

• Mitochondrial sequence
  cnmito.fa.gz (10k file)
  

• View download directory (includes old assemblies)
  http://www-sequence.stanford.edu/group/C.neoformans/files/

BAC end sequences

Total number of sequences: 5199
Total number of clones with both end sequences: 2378

• All BAC end sequences in one FASTA file
  sequences: alltraces030804.fa.gz (1.0M file)
  qualities: alltraces030804.fa.qual.gz (2.1M file)
  

• All BAC end traces (ABI chromatograms) in one trace archive
  alltraces030804.tar.gz(599M file)
  

• View download directory
  Includes trace tar archives and FASTA files split into smaller files by sequencing plate.
  http://www-sequence.stanford.edu/group/C.neoformans/bac_end_seqs/