Parsimony Approach to Test the Evolving Master Gene Hypothesis for Human Alu Repeats

Sridhar Ramachandran; Travis E. Doom; Michael L. Raymer; Dan E. Krane

doi:10.1109/BIBE.2006.253337

Parsimony Approach to Test the Evolving Master Gene Hypothesis for Human Alu Repeats

Sridhar Ramachandran, Travis E. Doom, Michael L. Raymer, Dan E. Krane

Research output: Contribution to conference › Poster

Abstract

The Alu family of Short interspersed repeats (SINEs) account for a significant portion of the "junk DNA" within the mammalian genome. Thousands of copies of Alu subfamilies are scattered essentially randomly through the human genome. The relative abundance of these repeats provides a rich fossil record of primate and human history. Since Alus have no known functionality, a great deal of ambiguity surrounds their amplification and evolution. Herein, using parsimony approach, we investigate the popular belief that the vast majority of Alu amplification is derived from a small subset of Alu master genes. Our results indicate that the classification of Alu subfamilies reported in literature is incomplete. Furthermore, we summarize some of the factors relevant to the use of the Alu family of repeats in bioinformatic assays.

Original language	American English
DOIs	https://doi.org/10.1109/BIBE.2006.253337
State	Published - Oct 1 2006
Event	Proceedings of the Sixth IEEE Symposium on BioInformatics and BioEngineering - Duration: Oct 1 2006 → …

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Conference	Proceedings of the Sixth IEEE Symposium on BioInformatics and BioEngineering
Period	10/1/06 → …

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Computer Sciences
Engineering

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10.1109/BIBE.2006.253337License: CC BY

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title = "Parsimony Approach to Test the Evolving Master Gene Hypothesis for Human Alu Repeats",

abstract = " The Alu family of Short interspersed repeats (SINEs) account for a significant portion of the {"}junk DNA{"} within the mammalian genome. Thousands of copies of Alu subfamilies are scattered essentially randomly through the human genome. The relative abundance of these repeats provides a rich fossil record of primate and human history. Since Alus have no known functionality, a great deal of ambiguity surrounds their amplification and evolution. Herein, using parsimony approach, we investigate the popular belief that the vast majority of Alu amplification is derived from a small subset of Alu master genes. Our results indicate that the classification of Alu subfamilies reported in literature is incomplete. Furthermore, we summarize some of the factors relevant to the use of the Alu family of repeats in bioinformatic assays.",

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AU - Ramachandran, Sridhar

AU - Doom, Travis E.

AU - Raymer, Michael L.

AU - Krane, Dan E.

PY - 2006/10/1

Y1 - 2006/10/1

N2 - The Alu family of Short interspersed repeats (SINEs) account for a significant portion of the "junk DNA" within the mammalian genome. Thousands of copies of Alu subfamilies are scattered essentially randomly through the human genome. The relative abundance of these repeats provides a rich fossil record of primate and human history. Since Alus have no known functionality, a great deal of ambiguity surrounds their amplification and evolution. Herein, using parsimony approach, we investigate the popular belief that the vast majority of Alu amplification is derived from a small subset of Alu master genes. Our results indicate that the classification of Alu subfamilies reported in literature is incomplete. Furthermore, we summarize some of the factors relevant to the use of the Alu family of repeats in bioinformatic assays.

AB - The Alu family of Short interspersed repeats (SINEs) account for a significant portion of the "junk DNA" within the mammalian genome. Thousands of copies of Alu subfamilies are scattered essentially randomly through the human genome. The relative abundance of these repeats provides a rich fossil record of primate and human history. Since Alus have no known functionality, a great deal of ambiguity surrounds their amplification and evolution. Herein, using parsimony approach, we investigate the popular belief that the vast majority of Alu amplification is derived from a small subset of Alu master genes. Our results indicate that the classification of Alu subfamilies reported in literature is incomplete. Furthermore, we summarize some of the factors relevant to the use of the Alu family of repeats in bioinformatic assays.

UR - https://corescholar.libraries.wright.edu/cse/281

U2 - 10.1109/BIBE.2006.253337

DO - 10.1109/BIBE.2006.253337

M3 - Poster

T2 - Proceedings of the Sixth IEEE Symposium on BioInformatics and BioEngineering

Y2 - 1 October 2006

ER -

Parsimony Approach to Test the Evolving Master Gene Hypothesis for Human Alu Repeats

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