Phylogenetic profiling of insertions and deletions in vertebrate genomes

Sagi Snir, Lior Pachter

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


Micro-indels are small insertion or deletion events (indels) that occur during genome evolution. The study of micro-indels is important, both in order to better understand the underlying biological mechanisms, and also for improving the evolutionary models used in sequence alignment and phylogenetic analysis. The inference of micro-indels from multiple sequence alignments of related genomes poses a difficult computational problem, and is far more complicated than the related task of inferring the history of point mutations. We introduce a tree alignment based approach that is suitable for working with multiple genomes and that emphasizes the concept of indel history. By working with an appropriately restricted alignment model, we are able to propose an algorithm for inferring the optimal indel history of homologous sequences that is efficient for practical problems. Using data from the ENCODE project as well as related sequences from multiple primates, we are able to compare and contrast indel events in both coding and non-coding regions. The ability to work with multiple sequences allows us to refute a previous claim that indel rates are approximately fixed even when the mutation rate changes, and allows us to show that indel events are not neutral. In particular, we identify indel hotspots in the human genome.

Original languageEnglish
Title of host publicationResearch in Computational Molecular Biology - 10th Annual International Conference, RECOMB 2006, Proceedings
Number of pages16
StatePublished - 2006
Externally publishedYes
Event10th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2006 - Venice, Italy
Duration: 2 Apr 20065 Apr 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3909 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference10th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2006

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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