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Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes

Snir, Sagi and Pachter, Lior (2006) Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. In: Research in Computational Molecular Biology. Lecture Notes in Computer Science. No.3909. Springer , Berlin, pp. 265-280. ISBN 978-3-540-33295-4.

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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.

Item Type:Book Section
Related URLs:
URLURL TypeDescription 10.1007/11732990_23DOIArticle
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2006 Springer-Verlag Berlin Heidelberg. SS and LP were partially funded by a grant from the NIH (R01: HG2362-3). We thank Yifat Felder, Benny Chor, and the anonymous referees for comments that improved the manuscript. We also thank Colin Dewey for his generous help
Funding AgencyGrant Number
NIHR01 HG2362-3
Series Name:Lecture Notes in Computer Science
Issue or Number:3909
Record Number:CaltechAUTHORS:20170307-163715632
Persistent URL:
Official Citation:Snir S., Pachter L. (2006) Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. In: Apostolico A., Guerra C., Istrail S., Pevzner P.A., Waterman M. (eds) Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science, vol 3909. Springer, Berlin, Heidelberg
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74874
Deposited By: George Porter
Deposited On:08 Mar 2017 15:55
Last Modified:15 Nov 2021 16:28

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