Klimke2009

CREATED: 201003141547 LINK: url:~/Modules/Literature/Klimke2009.pdf Title: The NCBI’s Protein Cluster Database

ProtClustDB contains curated and uncurated clusters of proteins grouped by sequence similarity

RefSeq project contains nonredundant sets of curated transcripts, gene and protein information in eukaryotic organisms, and gene and protein information in prokaryotes.

Goals of ProtClustDB:

routinely update RefSeq genomes with curated gene and protein information

• from ProtClustDB

provide a central aggregation source for information collected from a wide

• variety of sources that would be useful for scientists studying
• protein-level or genomic-level molecular functions

Method:

Proteins are separated into four groups: prokaryotes, phages, chloroplasts

• and mitochondria

Proteins are compared by sequence similarity using BLAST all against all

• (E-value cutoff 10E-05; effective length of the search space set to 5 x
• 10E8)

Each BLAST score is then modified by protein length x alignment length of

• the BLAST hit and the modified scores are sorted

Clusters (clique) consist of protein sets such that every member of the

• cluster hits every other protein member (reciprocal best hits by modified
• score).

For any given protein in the cluster, all other members of the cluster will have a greater modified score to the protein than any protein outside of the cluster.

ProtMap and cluster patterns show genomic neighborhoods.