Related Experiment Video
Updated: May 5, 2026
08:49
Self-Assembly of Microtubule Tactoids
Published on: June 23, 2022
4.6K
TIGRA: a targeted iterative graph routing assembler for breakpoint assembly
1Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
Genome Research
|December 6, 2013
Summary
We developed TIGRA, a novel assembler for next-generation sequencing data, to accurately characterize genomic structural variant breakpoints. TIGRA significantly improves the success rate and accuracy of assembling deletion and mobile element insertion breakpoints.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Next-generation sequencing (NGS) advances genomic structural variation studies.
- Characterizing structural variants at nucleotide resolution remains challenging due to short-read alignment and assembly limitations.
- Accurate breakpoint sequences are essential for discovering and functionally characterizing altered alleles.
Purpose of the Study:
- To develop an effective method for assembling structural variant breakpoints from NGS data.
- To improve the accuracy and success rate of breakpoint sequence determination.
- To facilitate the comprehensive study of genomic structural variations.
Main Methods:
- Development of a targeted iterative graph routing assembler (TIGRA).
- Implementation of novel data analysis routines for breakpoint assembly.
- Assessment using data from the 1000 Genomes Project.
Main Results:
- TIGRA accurately assembled the majority of deletion and mobile element insertion breakpoints.
- TIGRA demonstrated a substantively better success rate and accuracy compared to other algorithms.
- The method was successfully applied in the 1000 Genomes Project and other research initiatives.
Conclusions:
- TIGRA is an effective tool for accurate breakpoint assembly from NGS data.
- The developed assembler overcomes current limitations in characterizing structural variant sequences.
- TIGRA enhances the discovery and functional analysis of genomic structural variations.
Related Concept Videos
01:30Assembly of Signaling Complexes
4.7K
Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
4.7K
01:32Assembly of Complex Microtubule Structures
2.1K
Complex microtubule structures are present in resting cells and in dividing cells. In resting cells, they are responsible for maintaining the cellular architecture, tracks for intracellular transport, positioning of organelles, assembly of cilia and flagella. They mediate the bipolar spindle assembly for chromosomal segregation and positioning of the cell division plate in dividing cells. The formation of microtubule complex structures depends on the cell type, cell stage, and cell function.
2.1K
01:22Block Diagram Reduction
727
The process of deriving the transfer function of a control system often involves reducing its block diagram to a single block. This simplification can be achieved through a series of strategic operations, including relocating branch points and comparators. These operations preserve the overall function of the system while allowing for easier manipulation and combination of blocks.
The first step in this process is the identification and relocation of a branch point. A branch point, where a...
The first step in this process is the identification and relocation of a branch point. A branch point, where a...
727
01:18Assembly of Cytoskeletal Filaments
17.4K
Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...
17.4K
01:11IP3/DAG Signaling Pathway
12.5K
Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and...
12.5K
02:19The Spindle Assembly Checkpoint
2.9K
The spindle assembly checkpoint is a molecular surveillance mechanism ensuring the fidelity of chromosome segregation during anaphase. The checkpoint monitors the completion of all the prerequisite steps before chromosome segregation to determine whether the segregation process should proceed or be delayed.
Many proteins function together to control the spindle assembly checkpoint. Mutations affecting these proteins may allow cells to proceed into anaphase prematurely, resulting in the...
Many proteins function together to control the spindle assembly checkpoint. Mutations affecting these proteins may allow cells to proceed into anaphase prematurely, resulting in the...
2.9K