Pseudofam -- the pseudogene families database

URL:

http://pseudofam.pseudogene.org/

What you can do:

A database of pseudogene families based on the protein families from the Pfam database.

Highlights:

Pseudofam provides resources for analyzing the family structure of pseudogenes including query tools, statistical summaries and sequence alignments.
It contains more than 125,000 pseudogenes identified from 10 eukaryotic genomes and aligned within nearly 3000 families (approximately one-third of the total families in PfamA).
Pseudofam uses a large-scale parallelized homology search algorithm (implemented as an extension of the PseudoPipe pipeline) to identify pseudogenes.
Each identified pseudogene is assigned to its parent protein family and subsequently aligned to each other by transferring the parent domain alignments from the Pfam family.
Pseudogenes are also given additional annotation based on an ontology, reflecting their mode of creation and subsequent history.
The annotation highlights the association of pseudogene families with genomic features, such as segmental duplications.
In addition, pseudogene families are associated with key statistics, which identify outlier families with an unusual degree of pseudogenization.
The statistics also show how the number of genes and pseudogenes in families correlates across different species.

Keywords:

Literature & Tutorials:

PubMed Link: Pseudofam: the pseudogene families database

This record last updated: 01-21-2009