Benchmarking tools for the alignment of functional noncoding DNA

Benchmarking tools for the alignment of functional noncoding DNA

<p>Abstract</p> <p>Background</p> <p>Numerous tools have been developed to align genomic sequences. However, their relative performance in specific applications remains poorly characterized. Alignments of protein-coding sequences typically have been benchmarked against...

Full description

Bibliographic Details
Main Authors:	Stoye Jens, Bergman Casey M, Pollard Daniel A, Celniker Susan E, Eisen Michael B
Format:	Article
Language:	English
Published:	BMC 2004-01-01
Series:	BMC Bioinformatics
Online Access:	http://www.biomedcentral.com/1471-2105/5/6

Similar Items

GATA: a graphic alignment tool for comparative sequence analysis
by: Nix David A, et al.
Published: (2005-01-01)

An enhanced RNA alignment benchmark for sequence alignment programs
by: Steger Gerhard, et al.
Published: (2006-10-01)

DNAAlignEditor: DNA alignment editor tool
by: Guill Katherine E, et al.
Published: (2008-03-01)

Benchmarking long-read genome sequence alignment tools for human genomics applications
by: Jonathan LoTempio, et al.
Published: (2023-12-01)

Short Sequence Aligner Benchmarking for Chromatin Research
by: John Lawrence Carter, et al.
Published: (2023-09-01)

Benchmarking of alignment-free sequence comparison methods
by: Andrzej Zielezinski, et al.
Published: (2019-07-01)

Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals
by: Wentao Gong, et al.
Published: (2022-01-01)

Genomic selective constraints in murid noncoding DNA.
by: Daniel J Gaffney, et al.
Published: (2006-11-01)

CGAP-align: a high performance DNA short read alignment tool.
by: Yaoliang Chen, et al.
Published: (2013-01-01)

Protein sequence alignment analysis by local covariation: coevolution statistics detect benchmark alignment errors.
by: Russell J Dickson, et al.
Published: (2012-01-01)

Auto Sequencer: A DNA Sequence Alignment and Assembly Tool
by: Abhi Aggarwal, et al.
Published: (2018-06-01)

Quantifying the displacement of mismatches in multiple sequence alignment benchmarks.
by: Punto Bawono, et al.
Published: (2015-01-01)

Benchmarking in silico tools for the functional assessment of DNA variants using a set of strictly pharmacogenetic variants
by: Chua, Eng Wee, et al.
Published: (2019)

A benchmark study of sequence alignment methods for protein clustering
by: Yingying Wang, et al.
Published: (2018-12-01)

NONCODING CHLOROPLAST DNA VARIATION IN MEXICAN PINES
by: Delarosa, J, et al.
Published: (1995)

Patterns of selective constraints in noncoding DNA of rice
by: Keightley Peter D, et al.
Published: (2007-11-01)

Agreements ‘in the wild’: Standards and alignment in machine learning benchmark dataset construction
by: Isak Engdahl
Published: (2024-06-01)

OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
by: Searle Stephen MJ, et al.
Published: (2003-10-01)

Transfer of noncoding DNA drives regulatory rewiring in bacteria
by: Oren, Yaara, et al.
Published: (2015)

Simple structural differences between coding and noncoding DNA.
by: Kenneth J Locey, et al.
Published: (2011-02-01)

Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA
by: Annette Lien, et al.
Published: (2023-12-01)

Alignment of DNA sequences
by: Yang, Wen Wei
Published: (2008)

SparkEC: speeding up alignment-based DNA error correction tools
by: Roberto R. Expósito, et al.
Published: (2022-11-01)

New benchmark scenarios of electroweak baryogenesis in aligned two Higgs double models
by: Kazuki Enomoto, et al.
Published: (2022-09-01)

A new protein linear motif benchmark for multiple sequence alignment software
by: Poch Olivier, et al.
Published: (2008-04-01)

Computational identification and functional predictions of long noncoding RNA in Zea mays.
by: Susan Boerner, et al.
Published: (2012-01-01)

Benchmarking RNA Editing Detection Tools
by: David Rodríguez Morales, et al.
Published: (2023-08-01)

Realizing the significance of noncoding functionality in clinical genomics
by: Brian S. Gloss, et al.
Published: (2018-08-01)

Evolution and functions of long noncoding RNAs.
by: Ponting, C, et al.
Published: (2009)

The physiological function of long-noncoding RNAs
by: He Chen, et al.
Published: (2020-12-01)

Analysis of the Numerical Diffusion in Anisotropic Mediums: Benchmarks for Magnetic Field Aligned Meshes in Space Propulsion Simulations
by: Daniel Pérez-Grande, et al.
Published: (2016-11-01)

GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers.
by: Sebastian Jünemann, et al.
Published: (2014-01-01)

Assessing alignment-based taxonomic classification of ancient microbial DNA
by: Raphael Eisenhofer, et al.
Published: (2019-03-01)

Benchmarking DNA isolation methods for marine metagenomics
by: Alina Demkina, et al.
Published: (2023-12-01)

Innovative Tools of Educational Organization Development Management: Benchmarking
by: E. O. Okunkova
Published: (2020-12-01)

Improving Infinium MethylationEPIC data processing: re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods
by: Martin Bizet, et al.
Published: (2022-12-01)

Segmentation of DNA into Coding and Noncoding Regions Based on Recursive Entropic Segmentation and Stop-Codon Statistics
by: Daniel Nicorici, et al.
Published: (2004-01-01)

PhAST: pharmacophore alignment search tool
by: Schneider G, et al.
Published: (2009-06-01)

The Role of Small Noncoding RNA in DNA Double-Strand Break Repair
by: Iwona Rzeszutek, et al.
Published: (2020-10-01)

A Note of Zipf's Law, Natural Languages, and Noncoding DNA Regions
by: Niyogi, Partha, et al.
Published: (2004)