Identification of Protein Homologs and Domain Boundaries by Iterative Sequence Alignment

Dustin Schaeffer, Nick V. Grishin

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations


Evolutionary domains are protein regions with observable sequence similarity to other known domains. Here we describe how to use common sequence and profile alignment algorithms (i.e., BLAST, HHsearch) to delineate putative domains in novel protein sequences, given a reference library of protein domains. In this case, we use our database of evolutionary domains (ECOD) as a reference, but other domain sequence libraries could be used (e.g., SCOP, CATH). We describe our domain partition algorithm along with specific notes on how to avoid domain indexing errors when working with multiple data sources and software algorithms with differing outputs.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages10
StatePublished - 2019

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Homologs
  • Protein domains
  • Sequence alignment

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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