The software commonly used for assembly of shotgun sequence data has several limitations. One such limitation becomes obvious when repetitive sequences are encountered. Shotgun assembly is a difficult task, even for non-repetitive regions, but the use of quality assessments of the data and efficient matching algorithms have made it possible to assemble most sequences efficiently. In the case of highly repetitive sequences, however, these algorithms fail to distinguish between sequencing errors and single base differences in regions containing nearly identical repeats. None of the currently available fragment assembly programs are able to correctly assemble highly similar repetitive data, and we, therefore, present a novel shotgun assembly program, Tandem Repeat Assembly Program (TRAP). The main feature of this program is the ability to separate long repetitive regions from each other by distinguishing single base substitutions as well as insertions/deletions from sequencing errors. This is accomplished by using a novel multiple-alignment based analysis method. Since repeats are a common complication in most sequencing projects, this software should be of use for the whole sequencing community.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/s0169-2607(01)00194-8 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Tetrameric PilZ protein stabilizes stator ring in complex flagellar motor and is required for motility in .
Proc Natl Acad Sci U S A
January 2025
Chinese Academy of Sciences Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 511458, China.
Rotation of the bacterial flagellum, the first identified biological rotary machine, is driven by its stator units. Knowledge gained about the function of stator units has increasingly led to studies of rotary complexes in different cellular pathways. Here, we report that a tetrameric PilZ family protein, FlgX, is a structural component underneath the stator units in the flagellar motor of .
View Article and Find Full Text PDFLiquid-nano-liquid interface-oriented anisotropic encapsulation.
Proc Natl Acad Sci U S A
January 2025
Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, College of Chemistry and Materials, iChem (Collaborative Innovation Center of Chemistry for Energy Materials), Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200433, China.
Emulsion interface engineering has been widely employed for the synthesis of nanomaterials with various morphologies. However, the instability of the liquid-liquid interface and uncertain interfacial interactions impose significant limitations on controllable fabrications. Here, we developed a liquid-nano-liquid interface-oriented anisotropic encapsulation strategy for fabricating asymmetric nanohybrids.
View Article and Find Full Text PDFChromatin conformation, gene transcription, and nucleosome remodeling as an emergent system.
Sci Adv
January 2025
Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA.
In single cells, variably sized nanoscale chromatin structures are observed, but it is unknown whether these form a cohesive framework that regulates RNA transcription. Here, we demonstrate that the human genome is an emergent, self-assembling, reinforcement learning system. Conformationally defined heterogeneous, nanoscopic packing domains form by the interplay of transcription, nucleosome remodeling, and loop extrusion.
View Article and Find Full Text PDFGenetically Programmed Single-Component Protein Hydrogel for Spinal Cord Injury Repair.
Adv Sci (Weinh)
January 2025
Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, China.
Protein self-assembly allows for the formation of diverse supramolecular materials from relatively simple building blocks. In this study, a single-component self-assembling hydrogel is developed using the recombinant protein CsgA, and its successful application for spinal cord injury repair is demonstrated. Gelation is achieved by the physical entanglement of CsgA nanofibrils, resulting in a self-supporting hydrogel at low concentrations (≥5 mg mL).
View Article and Find Full Text PDFGenome-wide association study of varenicline-aided smoking cessation.
Nicotine Tob Res
January 2025
Department of Population Health Sciences, University of Leicester, Leicester, UK.
Introduction: Varenicline is an α4β2 nicotinic acetylcholine receptor partial agonist with the highest therapeutic efficacy of any pharmacological smoking cessation aid and a 12-month cessation rate of 26%. Genetic variation may be associated with varenicline response, but to date no genome-wide association studies of varenicline response have been published.
Methods: In this study, we investigated the genetic contribution to varenicline effectiveness using two electronic health record-derived phenotypes.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!