Tag: Rearrangement

BreakPointer Beta – Pinpoint Rearrangement Breakpoints using Paired end reads

BreakPointer Beta

:: DESCRIPTION

BreakPointer is a tool to pinpoint rearrangement breakpoints using paired end reads

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  BreakPointer

:: MORE INFORMATION

Citation

Drier Y, Lawrence MS, Carter SL, Stewart C, Gabriel SB, Lander ES, Meyerson M, Beroukhim R, Getz G.
Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability.
Genome Research 2012. Published in Advance November 2, 2012, doi:10.1101/gr.141382.112

MGRA 1.0 – Multiple Genome Rearrangements and Ancestors

MGRA 1.0.

:: DESCRIPTION

MGRA is a software for reconstruction of phylogenetic trees as well as ancestral genomes and applied it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum. MGRA relies on the new notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. In particular, we applied \MGRA to analyze the primate–rodent–carnivore controversy in mammalian phylogeny, i.e., the alternative between the primate–rodent and primate–carnivore clades. MGRA provided the rearrangement-based evidence, albeit limited, for the primate–carnivore clade as opposed to the currently favored primate–rodent clade.

::DEVELOPER

Max Alekseyev and Pavel A. Pevzner

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 MGRA

:: MORE INFORMATION

Citation:

Max Alekseyev, Pavel Pevzner
“Breakpoint Graphs and Ancestral Genome Reconstructions.”
Genome Res. 2009 May;19(5):943-57. Epub 2009 Feb 13.

 

M-GCAT 2.0 beta – Detect Highly Conserved Regions in Multiple Genomes with Rearrangements and Repeats

M-GCAT 2.0 beta

:: DESCRIPTION

M-GCAT is a tool for rapidly visualizing and aligning the most highly conserved regions in multiple (typically prokaryote) genomes. M-GCAT is based upon a highly efficient approach to anchor-based multiple genome comparison using a compressed suffix graph and thus can construct multiple genome alignment frameworks in closely related species usually in a few minutes. A couple of important limitations include (1) input sequences MUST be assembled, and (2) the comparison is reference-sequence biased.

::DEVELOPER

 the Algorithmics and Genetics Group 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 M-GCAT

:: MORE INFORMATION

Citation

T. Treangen and X. Messeguer.
M-GCAT: Interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species.
BMC Bioinformatics 2006, 7:433.

Exit mobile version