This unit provides an overview of issues involved in domain recognition in protein and DNA sequences. It opens with a discussion of the two primary methods of domain representation, namely consensus sequences and alignment matrices (e.g., the log-odds matrix). The unit continues with a brief overview of some of the resources available for identifying functional domains in nucleotide sequences (e.g., transcription factor binding sites). In addition, it reviews databases such as Pfam and InterPro, which are available for protein analysis.

Original languageEnglish
Pages (from-to)1-6
Number of pages6
JournalCurrent Protocols in Bioinformatics
Issue numberSUPPL. 34
StatePublished - Jun 2011


  • Functional domains
  • Promoters
  • Protein domains
  • Regulatory sites
  • Transcription factor binding sites


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