Cargando…

SBSA: an online service for somatic binding sequence annotation

Efficient annotation of alterations in binding sequences of molecular regulators can help identify novel candidates for mechanisms study and offer original therapeutic hypotheses. In this work, we developed Somatic Binding Sequence Annotator (SBSA) as a full-capacity online tool to annotate altered...

Descripción completa

Detalles Bibliográficos
Autores principales:	Jiang, Limin, Guo, Fei, Tang, Jijun, Yu, Hui, Ness, Scott, Duan, Mingrui, Mao, Peng, Zhao, Ying-Yong, Guo, Yan
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2021
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8500130/ https://www.ncbi.nlm.nih.gov/pubmed/34606615 http://dx.doi.org/10.1093/nar/gkab877

Ejemplares similares

SMDB: pivotal somatic sequence alterations reprogramming regulatory cascades
por: Jiang, Limin, et al.
Publicado: (2020)

Functional sequencing read annotation for high precision microbiome analysis
por: Zhu, Chengsheng, et al.
Publicado: (2018)

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
por: Wang, Kai, et al.
Publicado: (2010)

An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data
por: Shiraishi, Yuichi, et al.
Publicado: (2013)

Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies
por: Hestand, Matthew S., et al.
Publicado: (2010)

Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity
por: Philippe, Nicolas, et al.
Publicado: (2009)

Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens
por: Yost, Shawn E., et al.
Publicado: (2012)

Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing
por: Orabi, Baraa, et al.
Publicado: (2022)

Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks
por: Guo, Xingli, et al.
Publicado: (2013)

DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns
por: Clauwaert, Jim, et al.
Publicado: (2019)

HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins
por: Zhang, Fuhao, et al.
Publicado: (2023)

CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures
por: Islam, Shahidul, et al.
Publicado: (2017)

DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool
por: Motion, Graham B., et al.
Publicado: (2015)

Genotyping and annotation of Affymetrix SNP arrays
por: Lamy, Philippe, et al.
Publicado: (2006)

RATT: Rapid Annotation Transfer Tool
por: Otto, Thomas D., et al.
Publicado: (2011)

Robust analysis of 5′-transcript ends (5′-RATE): a novel technique for transcriptome analysis and genome annotation
por: Gowda, Malali, et al.
Publicado: (2006)

A new approach for annotation of transposable elements using small RNA mapping
por: El Baidouri, Moaine, et al.
Publicado: (2015)

T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data
por: Fiston-Lavier, Anna-Sophie, et al.
Publicado: (2015)

Transcriptome annotation using tandem SAGE tags
por: Rivals, Eric, et al.
Publicado: (2007)

Gene Ontology annotation quality analysis in model eukaryotes
por: Buza, Teresia J., et al.
Publicado: (2008)

GFam: a platform for automatic annotation of gene families
por: Sasidharan, Rajkumar, et al.
Publicado: (2012)

TransposonUltimate: software for transposon classification, annotation and detection
por: Riehl, Kevin, et al.
Publicado: (2022)

Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples
por: Sengupta, Subhajit, et al.
Publicado: (2016)

Sequence- and structural-selective nucleic acid binding revealed by the melting of mixtures
por: Shi, Xiaochun, et al.
Publicado: (2006)

REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes
por: Ndah, Elvis, et al.
Publicado: (2017)

De novo annotation and characterization of the translatome with ribosome profiling data
por: Xiao, Zhengtao, et al.
Publicado: (2018)

scMRMA: single cell multiresolution marker-based annotation
por: Li, Jia, et al.
Publicado: (2021)

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest
por: Uyar, Bora, et al.
Publicado: (2017)

Echtvar: compressed variant representation for rapid annotation and filtering of SNPs and indels
por: Pedersen, Brent S, et al.
Publicado: (2022)

A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data
por: Li, Shuya, et al.
Publicado: (2017)

Identification of target-binding peptide motifs by high-throughput sequencing of phage-selected peptides
por: Rentero Rebollo, Inmaculada, et al.
Publicado: (2014)

APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins
por: Sharan, Malvika, et al.
Publicado: (2017)

PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins
por: Laverty, Kaitlin U, et al.
Publicado: (2022)

Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence
por: Brejová, Broňa, et al.
Publicado: (2009)

Text-based over-representation analysis of microarray gene lists with annotation bias
por: Leong, Hui Sun, et al.
Publicado: (2009)

Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae
por: Atias, Nir, et al.
Publicado: (2016)

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
por: Meng, Guanliang, et al.
Publicado: (2019)

Information transduction capacity reduces the uncertainties in annotation-free isoform discovery and quantification
por: Deng, Yue, et al.
Publicado: (2017)

Exonuclease III protection assay with FRET probe for detecting DNA-binding proteins
por: Wang, Jinke, et al.
Publicado: (2005)

Sequence specificity of single-stranded DNA-binding proteins: a novel DNA microarray approach
por: Morgan, Hugh P., et al.
Publicado: (2007)

Cannot write session to /tmp/vufind_sessions/sess_i3jblmnmb8jle9q9rkvuo2f7ce