Cargando…

Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design

BACKGROUND: In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their sequences to proprietary assay design software, which was not met by existing software. Retrieval and formatting of sequences flanking each SNP, prior to assay desig...

Descripción completa

Detalles Bibliográficos
Autores principales:	Field, Helen I, Scollen, Serena A, Luccarini, Craig, Baynes, Caroline, Morrison, Jonathan, Dunning, Alison M, Easton, Douglas F, Pharoah, Paul DP
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2009
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711078/ https://www.ncbi.nlm.nih.gov/pubmed/19523221 http://dx.doi.org/10.1186/1471-2105-10-180

Ejemplares similares

SNP-RFLPing: restriction enzyme mining for SNPs in genomes
por: Chang, Hsueh-Wei, et al.
Publicado: (2006)

SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction
por: Abraham, Gad, et al.
Publicado: (2012)

PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes
por: Qu, Xiao-Jian, et al.
Publicado: (2019)

snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing
por: Al-Shahib, Ali, et al.
Publicado: (2013)

DROPA: DRIP-seq optimized peak annotator
por: Russo, Marco, et al.
Publicado: (2019)

Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants
por: Shih, Ching-Yu, et al.
Publicado: (2021)

GPAT: Retrieval of genomic annotation from large genomic position datasets
por: Krebs, Arnaud, et al.
Publicado: (2008)

mrSNP: Software to detect SNP effects on microRNA binding
por: Deveci, Mehmet, et al.
Publicado: (2014)

FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences
por: Banerjee, Sagnik, et al.
Publicado: (2021)

TSSAR: TSS annotation regime for dRNA-seq data
por: Amman, Fabian, et al.
Publicado: (2014)

Snat: a SNP annotation tool for bovine by integrating various sources of genomic information
por: Jiang, Jicai, et al.
Publicado: (2011)

SNPAAMapperT2K: A genome-wide SNP downstream analysis and annotation pipeline for species annotated with NCBI.tbl data files
por: Bai, Yongsheng
Publicado: (2014)

FRAMA: from RNA-seq data to annotated mRNA assemblies
por: Bens, Martin, et al.
Publicado: (2016)

Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data
por: Torkamaneh, Davoud, et al.
Publicado: (2017)

An ensemble approach to accurately detect somatic mutations using SomaticSeq
por: Fang, Li Tai, et al.
Publicado: (2015)

Magic-BLAST, an accurate RNA-seq aligner for long and short reads
por: Boratyn, Grzegorz M., et al.
Publicado: (2019)

SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms
por: Crowe, Mark L
Publicado: (2005)

ContextMap 2: fast and accurate context-based RNA-seq mapping
por: Bonfert, Thomas, et al.
Publicado: (2015)

SeqAnt: A web service to rapidly identify and annotate DNA sequence variations
por: Shetty, Amol Carl, et al.
Publicado: (2010)

Common variants in the ATM, BRCA1, BRCA2, CHEK2 and TP53 cancer susceptibility genes are unlikely to increase breast cancer risk
por: Baynes, Caroline, et al.
Publicado: (2007)

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data
por: Lin, Peijie, et al.
Publicado: (2017)

BugSeq: a highly accurate cloud platform for long-read metagenomic analyses
por: Fan, Jeremy, et al.
Publicado: (2021)

SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning
por: Balaji, Advait, et al.
Publicado: (2022)

‘apparent’: a simple and flexible R package for accurate SNP-based parentage analysis in the absence of guiding information
por: Melo, Arthur T. O., et al.
Publicado: (2019)

htSNPer1.0: software for haplotype block partition and htSNPs selection
por: Ding, Keyue, et al.
Publicado: (2005)

CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities
por: Kondratenko, Yulia, et al.
Publicado: (2020)

Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms
por: Doran, Anthony G, et al.
Publicado: (2013)

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
por: Li, Bo, et al.
Publicado: (2011)

Searching for SNPs with cloud computing
por: Langmead, Ben, et al.
Publicado: (2009)

SNP-VISTA: An interactive SNP visualization tool
por: Shah, Nameeta, et al.
Publicado: (2005)

SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data
por: Pattnaik, Swetansu, et al.
Publicado: (2014)

SNP-PHAGE – High throughput SNP discovery pipeline
por: Matukumalli, Lakshmi K, et al.
Publicado: (2006)

Eval: A software package for analysis of genome annotations
por: Keibler, Evan, et al.
Publicado: (2003)

AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip™ expression arrays with respect to SNPs
por: Kumari, Sunita, et al.
Publicado: (2007)

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
por: Zhu, Lihua J, et al.
Publicado: (2010)

MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
por: Khomtchouk, Bohdan B., et al.
Publicado: (2016)

Heterogeneous computing architecture for fast detection of SNP-SNP interactions
por: Sluga, Davor, et al.
Publicado: (2014)

dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments
por: Petukhov, Viktor, et al.
Publicado: (2018)

Common variation in EMSY and risk of breast and ovarian cancer: a case-control study using HapMap tagging SNPs
por: Benusiglio, Patrick R, et al.
Publicado: (2005)

Software for optimization of SNP and PCR-RFLP genotyping to discriminate many genomes with the fewest assays
por: Gardner, Shea N, et al.
Publicado: (2005)

Cannot write session to /tmp/vufind_sessions/sess_3d46ru4ovmeijhua2464ltdt6c