Sequence - and Structural Databases at the IT Services.
All Databases available on the zisgi are in the directory: /data Sequence Databases Nucleic Acid Sequences We provide Nucleic Acid and Amino Acid Sequences in GCG (non binary) format. Our main Nucleic Acid database is the EMBL Database. It is updated weekly. We provide the Genbank as "Exclusion Set". This means that it contains all entries that were not in the latest EMBL Full Release. EMBL and The Genbank "Exclusion Set" are updated weekly. For the present EMBL Release notes click here For the present Genbank Release notes click here Non Redundant Databases For Blast and Fasta searches we provide non redundant DNA and Aminoacid Databases. The databases are updated weekly. Amino Acid Sequences We supply different Amino Acid Databases. Swissprot SP Documentation Trembl (translated EMBL) Releasenotes Pir (1-4) Documentation NRL_3D (Brookhaven) Documentation For information on ALL the present versions click here Farm files Almost all of the GCG-Databases are composed of different database subsets. On the zisgi we offer the possibility to search these different subsets seperately. It is much more efficient to search certain subsets of the databases than to search whole databases. E.g. if you want to search bacterial sequences, it is senseless to search the whole Genembl (default) database as it has Millions of sequences that don't interest you. GCG offers the possibility to generate so called farm files. These farm files contain different database subsets and you can address the farm files as if they were real databases. One example is the bacterial farm. So, in the above example, please don't use the default: Genembl:* but use the bacterial database subsections bacterial:* instead. To find out which farm files we provide please go to the page: Farm files of GCG 10 Structural Databases As structural database we provide the PDB Database. This Database contains Structures of Protein, DNA, and RNA Molecules. Most coordinates were obtained from X-Ray or NMR studies. The Database is maintained at the Brookhaven National Laboratory. (DON'T use the ls command in the directory /data/pdb/pdb_data. It takes ages !) General Information The filename format of the pdb-files is pdb[1-9]xxx.ent