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Rescooped by Mel Melendrez-Vallard from Bioinformatics Training
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abSYNTH Bioinformatics Tools

abSYNTH Bioinformatics Tools | Bioinformatics Software: Sequence Analysis | Scoop.it

Via Costas Bouyioukos, Pedro Fernandes
Mel Melendrez-Vallard's insight:

well that's neat.

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Costas Bouyioukos's curator insight, March 26, 2014 4:31 AM

Our tutorial on tools for the systematic analysis of periodicities on genomic sequences run (almost) smoothly yesterday at the 2014 aSSB Evry Thematic School.

 

Find the tools of MEGA team on iSSB webtools server https://absynth.issb.genopole.fr/Bioinformatics/

under the systems biology section.
(registration, simple and free, is required)

Bioinformatics Software: Sequence Analysis
Research and postings on the latest in bioinformatic analysis software that's out there/published and open source. Let's not re-invent the wheel. Disclaimer: I do not promote one software over the next, you'll have to evaluate software on your own.
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Bioinformatics tools extracted from a typical mammalian genome project | The OpenHelix Blog

Bioinformatics tools extracted from a typical mammalian genome project | The OpenHelix Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
In this extended blog post, I describe my efforts to extract the information about bioinformatics-related items from a recent genome sequencing paper, and the
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SNP-SIG 2013: the state of the art of genomic variant interpretation

OB: SNP-SIG 2013: the state of the art of genomic variant interpretation: Contact: yanab@rci.rutgers.edu or em... http://t.co/UXP1yE5oJv
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Reconciling differential gene expression data with molecular interaction networks

RT @markgerstein: Reconciling differential gene expression w/...#networks http://t.co/q1yUFU2JvC Propagating this across interactions finds…
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Motif mining based on network space compression

A network motif is a recurring subnetwork within a network, and it takes on certain functions in practical biological macromolecule applications.
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MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification

Background:
Sequencing datasets consist of a finite number of reads which map to specific regions of a reference genome. Most effort in modeling these datasets focuses on the detection of univariate differentially expressed genes.
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Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

Background:
Genetic studies are increasingly based on short noisy next generation scanners. Typically complete DNA sequences are assembled by matching short NextGen sequences against reference genomes.
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Generate an RNA-seq count matrix with featureCounts

Featurecounts is the fastest read summarization tool currently out there and has some great features which make it superior to HTSeq or Bedtools multicov.
FeatureCounts takes GTF files as an annotation.
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Fast and robust group-wise eQTL mapping using sparse graphical models

Background:
Genome-wide expression quantitative trait loci (eQTL) studies have emerged as a powerful tool to understand the genetic basis of gene expression and complex traits.
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SubPatCNV: approximate subspace pattern mining for mapping copy-number variations

Background:
Many DNA copy-number variations (CNVs) are known to lead to phenotypic variations and pathogenesis.
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Extending reference assembly models

The human genome reference assembly is crucial for aligning and analyzing sequence data, and for genome annotation, among other roles.
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microRNA aligners compared

Alignment of microRNA to the genome poses a particular challenge because the reads are short, and some microRNAs are nearly identical.
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ERD: a fast and reliable tool for RNA design including constraints

Background:
The function of an RNA in cellular processes is directly related to its structure.
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TagDust2: a generic method to extract reads from sequencing data

Background:
Arguably the most basic step in the analysis of next generation sequencing data (NGS) involves the extraction of mappable reads from the raw reads produced by sequencing instruments.
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DARPA sets out to automate research - Science Careers Blog (subscription)

DARPA sets out to automate research Science Careers Blog (subscription) Building a system that actually produces scientific insight will not be easy, says computational biologist Larry Hunter of Smart Information Flow Technologies in Minneapolis,...
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An Integrative Approach to Predicting the Functional Effects of Non-Coding and Coding Sequence Variation

Recent @BBSRC @MRCcomms @EPSRC funded @BristolUni article on genome sequence variation published #OA @OxfordJournals http://t.co/g5MvEd5o9j
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Comparative evaluation of gene set analysis approaches for RNA-Seq data

Background:
Over the last few years transcriptome sequencing (RNA-Seq) has almost completely taken over microarrays for high-throughput studies of gene expression.
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Erratum: An iteration normalization and test method for differential expression analysis of RNA-seq data

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Evaluation of de novo transcriptome assemblies from RNA-Seq data

De novo RNA-Seq assembly facilitates the study of transcriptomes for species without sequenced genomes, but it is challenging to select the most accurate assembly in this context.
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ALLMAPS: robust scaffold ordering based on multiple maps

The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly.
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Nonparametric Bayesian clustering to detect bipolar methylated genomic loci

Background:
With recent development in sequencing technology, a large number of genome-wide DNA methylation studies have generated massive amounts of bisulfite sequencing data.
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Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data

Background:
Single-molecule techniques have emerged as incisive approaches for addressing a wide range of questions arising in contemporary biological research [
1-4].
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Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics

While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of this data rely upon parallelization strategies that have limited scalability, complex implementation and lack...
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Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

Background:
Recent assays for individual-specific genome-wide DNA methylation profiles have enabled epigenome-wide association studies to identify specific CpG sites associated with a phenotype.
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MDAT- Aligning multiple domain arrangements

Background:
Proteins are composed of domains, protein segments that fold independently from the rest of the protein and have a specific function.
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Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach

Background:
Familial binding profiles (FBPs) represent the average binding specificity for a group of structurally related DNA-binding proteins.
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Frontiers | Computational Prediction of miRNA Genes from Small RNA Sequencing Data | Bioinformatics and Computational Biology

Next-generation sequencing now for the first time allows researchers to gauge the depth and variation of entire transcriptomes. However, now as rare transcripts can be detected that are present in ...
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