Parsimony and likelihood reconstruction of human segmental duplications
نویسندگان
چکیده
منابع مشابه
Parsimony and likelihood reconstruction of human segmental duplications
MOTIVATION Segmental duplications > 1 kb in length with >or= 90% sequence identity between copies comprise nearly 5% of the human genome. They are frequently found in large, contiguous regions known as duplication blocks that can contain mosaic patterns of thousands of segmental duplications. Reconstructing the evolutionary history of these complex genomic regions is a non-trivial, but importan...
متن کاملA Parsimony Approach to Analysis of Human Segmental Duplications
Segmental duplications are abundant in the human genome, but their evolutionary history is not well-understood. The mystery surrounding them is due in part to their complex organization; many segmental duplications are mosaic patterns of smaller repeated segments, or duplicons. A two-step model of duplication has been proposed to explain these mosaic patterns. In this model, duplicons are copie...
متن کاملRecent segmental duplications in the human genome.
Primate-specific segmental duplications are considered important in human disease and evolution. The inability to distinguish between allelic and duplication sequence overlap has hampered their characterization as well as assembly and annotation of our genome. We developed a method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun s...
متن کاملParsimony, likelihood, and simplicity
The latest charge against parsimony in phylogenetic inference is that it involves estimating too many parameters. The charge is derived from the fact that, when each character is allowed a branch length vector of its own (instead of the homogeneous branch lengths assumed in current likelihood models), the results for likelihood and parsimony are identical. Parsimony, however, can also be derive...
متن کاملSignals of Historical Interlocus Gene Conversion in Human Segmental Duplications
Standard methods of DNA sequence analysis assume that sequences evolve independently, yet this assumption may not be appropriate for segmental duplications that exchange variants via interlocus gene conversion (IGC). Here, we use high quality multiple sequence alignments from well-annotated segmental duplications to systematically identify IGC signals in the human reference genome. Our analysis...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2010
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btq368