Article

Pseudofam: The pseudogene families database

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
Nucleic Acids Research (Impact Factor: 9.11). 11/2008; 37(Database issue):D738-43. DOI: 10.1093/nar/gkn758
Source: PubMed

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.

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    • "Additionally, pseudogene transcripts corresponding to CALM2 (calmodulin 2 phosphorylase kinase, delta), TOMM40 (translocase of outer mitochondrial membrane 40), NONO (non-POU domain-containing, octamer-binding), DUSP8 (dual-specificity phosphatase 8), PERP (TP53 apoptosis effector), and YES (v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1), etc. were observed in more than 50 samples each, which were further validated by pseudogene-specific RT-PCR followed by Sanger sequencing (Table S4). Further, because our RNA-Seq compendium comprises 35-to 45-mer short sequence reads that largely generated short sequence clusters not optimal for available pseudogene analysis tools such as Pseudopipe (Zhang et al., 2006) and Pseudofam (Lam et al., 2009) used in generating ENCODE and Yale databases , we carried out a direct query of individual clusters against the human genome (hg18) using the BLAT tool from UCSC, which is ideally suited for short sequence alignment searches (Kent, 2002). Based on this ''custom'' analysis, or simply BLAT (Figure S2A), we were able to independently assign 1,888 clusters representing 1,820 unique pseudogenes to unique genomic locations. "
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    Cell 06/2012; 149(7):1622-34. DOI:10.1016/j.cell.2012.04.041 · 33.12 Impact Factor
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    • "Although the function of most ncRNAs is unknown, some have been implicated in the regulation of disease, stress conditions, imprinting, gene silencing and enhancer regulation (Costa, 2007; Orom & Shiekhattar, 2011). Pseudogenes that lack protein-coding potential can be considered to be a type of ncRNA (Lam et al., 2009). Pseudogenes show sequence similarity to some functional parental genes (Muro et al., 2011). "
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    BMC Genetics 04/2010; 11:22. DOI:10.1186/1471-2156-11-22 · 2.36 Impact Factor
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