The Pfam Protein Families Database

No abstract is available for this paper.

• Publication year

  2000

• Venue

  Nucleic Acids Res.

• Publication date

  Unknown publication date

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/nar/28.1.263PMID 10592242PMCID PMC102420
• 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.

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  2000cited by this paper
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  1999cited by this paper
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  1999cited by this paper
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  1994cited by this paper
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  1987cited by this paper
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  1984cited by this paper
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