PseudoPipe: an automated pseudogene identification pipeline

No abstract is available for this paper.

• Publication year

  2006

• Venue

  Bioinform.

• Publication date

  2006-06-15

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btl116PMID 16574694
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Large-scale analysis of pseudogenes in the human genome.

  2004cited by this paper
• Comparative analysis of processed pseudogenes in the mouse and human genomes.

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• Acknowledgements

  2003cited by this paper
• Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.

  2003influential reference
• An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene

  2003cited by this paper
• Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome.

  2002cited by this paper
• Vertebrate pseudogenes

  2000cited by this paper
• Comparison of DNA sequences with protein sequences.

  1997cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997cited by this paper

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  2021influential citation
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