Sequence and Motif Databases

Table of major sequence, whole genome and motif databases maintained.

Complete directory structure of sequence databases on the BlastMachine and UNIX fileserver.

Directory structure with file listings of genome databases.

A combined listing of directory structures included those on the GeneMatcher2 with instructions.

NCBI BlastDB filenames with descriptions.

TIGR sequence database filenames with descriptions.

Pfam Details (on GeneMatcher2 only)

Pfam website (Washington University)
Pfam ftp site (Washington University)

Note - In the GeneMatcher2, Pfam is a query set, not a database set. It is distributed in two alignment models, global and local (See the Pfam release notes for global vs local models).

• Pfam_ls - All global (ls mode) Pfam-A HMMs.
• Pfam_fs - All local (fs mode) Pfam-A HMMs

Current Queryset names (release 16, November 2004):

Pfam16.0_fs_local (local model)
Pfam16.0_ls_global (global model)

 

Other Database Details

EMBL

IPI - International Protein Index. This is a non-redundant combination of SWISS-PROT, TrEMBL, RefSeq and Ensembl.

DOE Joint Genome Institute

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