Next Gen Sequencing (NGS) and Bioinformatics at UVic
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Next Gen Sequencing (NGS) and Bioinformatics at UVic
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BL!P: BLAST in Pivot

BL!P: BLAST in Pivot | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
BL!P, or BLAST in Pivot, is a bioinformatics program that aligns biological sequences and processes the results for visualization in Pivot.

BL!P was developed using C# and .NET 4.0, and uses the Microsoft Biology Foundation toolkit.

Via Mohamed Nadhir Djekidel
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BMC Bioinformatics | Abstract | Assessing statistical significance in causal graphs

Causal graphs are an increasingly popular tool for the analysis of biological datasets.
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Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads

MT @SAGRudd: Positional correlation improves reconstruction of full-lngth transcripts & alt isoforms frm noisy #RNASeq http://t.co/AdvAHoA5...
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Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

High-throughput sequencing (HTS) technologies have made low-cost sequencing of large numbers of samples commonplace. An explosion in the type, not just number, of sequencing experiments has also taken place including genome re-sequencing, population-scale variation detection, whole transcriptome sequencing and genome-wide analysis of protein-bound nucleic acids.

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BMC Genomics | Abstract | Whole-Genome Sequencing and Genetic Variant Analysis of a Quarter Horse Mare

The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project.
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BMC Bioinformatics | Abstract | PANDAseq: PAired-eND Assembler for Illumina sequences

Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene.
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htSeqTools: high-throughput sequencing quality control, processing and visualization in R

Summary: We provide a Bioconductor package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies.

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Public Cloud Databases For Bioinformatics

Public Cloud Databases For Bioinformatics | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
At some point in the evolution of every biopharmaceutical company, they're faced with the problem of finding new targets to keep their pipeline fully loaded.  Usually, they've exhausted the existi...

Via Sandrine Palcy
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BMC Genomics Ac/Ds-transposon activation tagging in poplar: a powerful tool for gene discovery

Rapid improvements in the development of new sequencing technologies have led to the availability of genome sequences of more than 300 organisms today.
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Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

With the development of next-generation sequencing (NGS) techniques, many software tools have emerged for the discovery of novel microRNAs (miRNAs) and for analyzing the miRNAs expression profiles. An overall evaluation of these diverse software tools is lacking. In this study, we evaluated eight software tools based on their common feature and key algorithms.

 

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Genome Canada - 2012 Large-Scale Applied Research Project Competition

Genome Canada - 2012 Large-Scale Applied Research Project Competition | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
GenomeCanada announced 2012 Large-Scale Applied Research Project Competition worth $67.5M http://t.co/A9ITsTEv #genomics #bioinformatics...
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ProfileGrid.org

ProfileGrid.org | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
Large multiple sequence alignments (MSAs) are taxing current visualization methods such as the traditional stacked sequence depiction. ProfileGrids are a new paradigm for visualizing and analyzing MSAs in a concise representation.
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DNA: An introduction to nanopore sequencing - Analytes and Applications: DNA, RNA, proteins - Technology - Oxford Nanopore Technologies

"Strand sequencing" is a technique that passes intact DNA polymers through a protein nanopore, sequencing in real time as the DNA translocates the pore. Oxford Nanopore intends to commercialise this technology independently within 2012.

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Movies - News - Oxford Nanopore Technologies

Movies - News - Oxford Nanopore Technologies | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
Oxford Nanopore videos look nice http://t.co/65nERTN1 will the proprietary protein nanopores & processive enzyme work?
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RNA-Seq Atlas – A reference database for gene expression profiling in normal tissue by next generation sequencing

RNA-Seq Atlas – A reference database for gene expression profiling in normal tissue by #NGSeq / #RNASeq = #awesome http://t.co/4IACsepF...
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Would you like to help curate this topic?

Guest curators:

Nik Veldhoen

Ed Rybicki (U of Cape Town; http://bit.ly/wYBezD)

Visit Ed's Scoop.it: http://www.scoop.it/t/virology-news

 

Also see: http://www.scoop.it/t/viral-bioinformatics

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BMC Bioinformatics | Abstract | CodingMotif: Exact Determination of Overrepresented Nucleotide Motifs in Coding Sequences

It has been increasingly appreciated that coding sequences harbor regulatory sequence motifs in addition to encoding for protein. These sequence motifs are expected to be overrepresented in nucleotide sequences bound by a common protein or small RNA.
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Sequencing set to alter clinical landscape : Nature News & Comment

Sequencing set to alter clinical landscape : Nature News & Comment | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
Access to whole genomes shifts potential for diagnosis, but poses challenges for doctors and regulators.
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A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq

A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq


Via Neelima Sinha
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Online bioinformatics tools

Online bioinformatics tools | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it

This is the space where I collect the diverse online bioinformatics resources and tools that I find useful.

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Improving bioinformatic pipelines for exome variant calling

MRT “@GenomeMedicine: Improving bioinformatic pipelines for #exome seq data analysisi http://t.co/p4yqk6MO (subs) #genomics” @rdbagnall...

Via Dr Richard Badge
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Bioconductor - Home

About Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 516 software packages, and an active user community. Bioconductor is also available as an Amazon Machine Image (AMI).

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HandAlign: Bayesian multiple sequence alignment, phylogeny, and ancestral reconstruction

Summary: We describe handalign, a software package for Bayesian reconstruction of phylogenetic history.

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A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

RT @genetics_blog: Comparison of methods for detecting differentially expressed genes from RNA-seq data http://t.co/dbiSsnmX #bioinformatics...
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