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Pseudofam: the pseudogene families database
- Source :
- Nucleic Acids Research
- Publication Year :
- 2008
- Publisher :
- Oxford University Press (OUP), 2008.
-
Abstract
- Pseudofam (http://pseudofam.pseudogene.org) is a database of pseudogene families based on the protein families from the Pfam database. It provides resources for analyzing the family structure of pseudogenes including query tools, statistical summaries and sequence alignments. The current version of Pseudofam 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. In particular, our 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. Overall, they highlight the fact that housekeeping families tend to be enriched with a large number of pseudogenes.
- Subjects :
- Protein family
Pseudogene
Genomics
Sequence alignment
Biology
computer.software_genre
Genome
Homology (biology)
03 medical and health sciences
Annotation
0302 clinical medicine
Databases, Genetic
Genetics
Animals
Humans
030304 developmental biology
Segmental duplication
Internet
0303 health sciences
Database
Proteins
Articles
Data Interpretation, Statistical
Sequence Alignment
computer
Pseudogenes
030217 neurology & neurosurgery
Subjects
Details
- ISSN :
- 13624962 and 03051048
- Volume :
- 37
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research
- Accession number :
- edsair.doi.dedup.....afa2c90b1c20e5a422e0a033ee0e5f74