Cargando…

ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments

Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide consensus-based summaries of the sequences in the alignment. Consequently, individual sequences cannot be identified in the visualization and c...

Descripción completa

Detalles Bibliográficos
Autores principales:	Schwarz, Roland F., Tamuri, Asif U., Kultys, Marek, King, James, Godwin, James, Florescu, Ana M., Schultz, Jörg, Goldman, Nick
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2016
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856975/ https://www.ncbi.nlm.nih.gov/pubmed/26819408 http://dx.doi.org/10.1093/nar/gkw022

Ejemplares similares

Alignment Modulates Ancestral Sequence Reconstruction Accuracy
por: Vialle, Ricardo Assunção, et al.
Publicado: (2018)

Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs
por: Kultys, Marek, et al.
Publicado: (2014)

Alvis: a tool for contig and read ALignment VISualisation and chimera detection
por: Martin, Samuel, et al.
Publicado: (2021)

Epidaurus: aggregation and integration analysis of prostate cancer epigenome
por: Wang, Liguo, et al.
Publicado: (2015)

BatAlign: an incremental method for accurate alignment of sequencing reads
por: Lim, Jing-Quan, et al.
Publicado: (2015)

Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments
por: Miga, Karen H., et al.
Publicado: (2015)

EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences
por: Ge, Xinzhou, et al.
Publicado: (2019)

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming
por: Mukherjee, Srayanta, et al.
Publicado: (2009)

A Mutation–Selection Model of Protein Evolution under Persistent Positive Selection
por: Tamuri, Asif U, et al.
Publicado: (2021)

STRALCP—structure alignment-based clustering of proteins
por: Zemla, Adam, et al.
Publicado: (2007)

Single-step genome engineering in the bee gut symbiont Snodgrassella alvi
por: Lariviere, Patrick J., et al.
Publicado: (2023)

Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq
por: Hartley, Stephen W., et al.
Publicado: (2016)

Hobbes: optimized gram-based methods for efficient read alignment
por: Ahmadi, Athena, et al.
Publicado: (2012)

Comparison of alignment software for genome-wide bisulphite sequence data
por: Chatterjee, Aniruddha, et al.
Publicado: (2012)

Alignment free identification of clones in B cell receptor repertoires
por: Lindenbaum, Ofir, et al.
Publicado: (2020)

Meander: visually exploring the structural variome using space-filling curves
por: Pavlopoulos, Georgios A., et al.
Publicado: (2013)

R-Coffee: a method for multiple alignment of non-coding RNA
por: Wilm, Andreas, et al.
Publicado: (2008)

Incorporating sequence quality data into alignment improves DNA read mapping
por: Frith, Martin C., et al.
Publicado: (2010)

A mostly traditional approach improves alignment of bisulfite-converted DNA
por: Frith, Martin C., et al.
Publicado: (2012)

Sim4cc: a cross-species spliced alignment program
por: Zhou, Leming, et al.
Publicado: (2009)

NGC: lossless and lossy compression of aligned high-throughput sequencing data
por: Popitsch, Niko, et al.
Publicado: (2013)

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
por: Liao, Yang, et al.
Publicado: (2013)

Boiler: lossy compression of RNA-seq alignments using coverage vectors
por: Pritt, Jacob, et al.
Publicado: (2016)

BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome
por: Huisman, Sjoerd M.H., et al.
Publicado: (2017)

Selection of DNA nanoparticles with preferential binding to aggregated protein target
por: Ruff, Laura E., et al.
Publicado: (2016)

Finding regulatory DNA motifs using alignment-free evolutionary conservation information
por: Gordân, Raluca, et al.
Publicado: (2010)

Using a priori knowledge to align sequencing reads to their exact genomic position
por: Böttcher, René, et al.
Publicado: (2012)

Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques
por: Ortuño, Francisco M., et al.
Publicado: (2013)

Graph-based modeling of tandem repeats improves global multiple sequence alignment
por: Szalkowski, Adam M., et al.
Publicado: (2013)

RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment
por: Zhong, Cuncong, et al.
Publicado: (2010)

Use of ChIP-Seq data for the design of a multiple promoter-alignment method
por: Erb, Ionas, et al.
Publicado: (2012)

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model
por: Wang, Liguo, et al.
Publicado: (2013)

RNA global alignment in the joint sequence–structure space using elastic shape analysis
por: Laborde, Jose, et al.
Publicado: (2013)

Jointly aligning a group of DNA reads improves accuracy of identifying large deletions
por: Shrestha, Anish M S, et al.
Publicado: (2018)

Effective and scalable single-cell data alignment with non-linear canonical correlation analysis
por: Hu, Jialu, et al.
Publicado: (2021)

Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
por: Chivian, Dylan, et al.
Publicado: (2006)

Improved search heuristics find 20 000 new alignments between human and mouse genomes
por: Frith, Martin C., et al.
Publicado: (2014)

STAR3D: a stack-based RNA 3D structural alignment tool
por: Ge, Ping, et al.
Publicado: (2015)

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads
por: Liao, Yang, et al.
Publicado: (2019)

Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment
por: Tang, Kaihao, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_t6sjer75njefu8d85nhmgsn2ub