Accessing Rat FTP Data

Sequences are available in a number of formats.

The Genome assembly is available from ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Rnorvegicus/ as linearized chromosome files in the chromosome/ directory and as contig files in the contigs/ directory. Each of these directories contains .fasta and .qual files for each sequence. In addition, the contigs directory contains .agp files that give the position of each contig in the chromosome assemblies, and a bacfile that gives the BAC association information for each contig.

Other types of sequences are available from ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Rnorvegicus/:

Clone based assemblies are accessioned in GenBank and available here as .fasta files. Assemblies of BAC clones with BAC sequence reads only are found in the fasta/ directory. Assemblies of BAC clones with the overlapping whole genome shotgun sequence reads, or enriched BACs, are found in the atlas/ directory.

Blast formatted databases for enriched BAC assemblies and Superbactigs are available in the blast/ directory.

Individual sequence traces are available from the NCBI Trace Archive.