Monthly Archives: November 2010

Free & Open Environment for RNA-seq analysis: Galaxy

Free & Open Environment for RNA-seq analysis: Galaxy

The Galaxy Team announced yesterday that the first free public resource for RNA-seq analysis is now available through the Galaxy public server at http://usegalaxy.org . Galaxy now supports both Tophat and Cufflinks and also provides useful utilities for manipulating and ...

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Transcriptomics Improves Genomics…

Bacillus anthracis genome organization in light of whole transcriptome sequencing Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence ...

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HMMSplicer – for finding splice junctions in RNA-Seq data

The DeRisi lab is pleased to release HMMSplicer to the community. This open-source software package discovers splice junctions in RNA-Seq datasets without using gene models. HMMSplicer was benchmarked on publicly available A. thaliana, H. sapiens, and P. falciparum datasets and ...

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RNA-Seq libraries from ten nanograms of total RNA

Highly consistent, fully representative mRNA-Seq libraries from ten nanograms of total RNA Biotechniques – Reports Sengupta, S et al. Preparation of an Illumina sequencing library for gene expression analysis (mRNA-Seq) requires microgram amounts of starting total RNA or PCR-based amplification. ...

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RNA-Seq Poll Results

Which sequencing platform/technology is best suited for RNA-Seq applications? Platform                                  Votes Roche/454 – GS FLX                        4 Illumina – Genome Analyzer            12 Illumina – HiSeq                             16 Applied Biosystems – SOLiD            6 Helicos – HeliScope                         2 Pacific Biosciences                          2 Total Votes                                   42

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Microarrays & Sequencing Assume Supporting Roles

from GEN by Richard A. Stein, M.D., Ph.D. Which Tool Is Best Depends on the Question Asked and the System Being Surveyed While techniques available in the past allowed only a limited number of genes to be examined at one ...

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MISO – infer isoform regulation from RNA-seq data

Through alternative splicing, most human genes express multiple isoforms that often differ in function. To infer isoform regulation from high-throughput sequencing of cDNA fragments (RNA-seq), we developed the mixture-of-isoforms (MISO) model, a statistical model that estimates expression of alternatively spliced ...

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Transcriptome Sequencing of 750 Marine Microbes

Sequencing Project Aims to Uncover New Knowledge About Ocean Microeukaryotes SANTA FE, N.M.–(BUSINESS WIRE)–The National Center for Genome Resources (NCGR) and the Gordon and Betty Moore Foundation’s (GBMF) Marine Microbiology Initiative (MMI) today announced a new research program to sequence ...

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