#RNA-seq analysis of single bovine blastocysts

Background: Use of #RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available from individual embryos has made this a challenging prospect. Results: We report here the first application of #RNA-Seq for the analysis of individual blastocysts gene expression, SNP detection, and characterization of allele specific expression (ASE). #RNA was extracted from single bovine blastocysts (n = 5), amplified, and analyzed using high-throughput sequencing. Approximately 38 million sequencing reads were generated per embryo and 9,489 known bovine genes were found to be expressed, with a high correlation of expression levels between samples (r > 0.97). Transcriptomic data was analyzed to identify SNP in expressed genes, and individual SNP were examined to characterize allele specific expression. Expressed biallelic SNP variants with allelic imbalances were observed in 473 SNP, where one allele represented between 65-95% of a variant’s transcripts. Conclusions: This study represents the first application of #RNA-seq technology in single bovine embryos allowing a representation of the embryonic transcriptome and the analysis of transcript sequence variation to describe specific allele expression. http://bit.ly/ZkjcLB #BMC

eXpress • Home

bio.math.berkeley.edu 200) && (this.width >= this.height) ? 200: true); max-height: 200px; height: expression((this.height > 200) && (this.height >= this.width) ? 200: true); border: none;’/> eXpress is a general quantification tool for target DNA/#RNA sequences. While its primary use currently is #RNA-Seq it has the potential for applications in many other areas including as allele-specific expression and metgenomics. What makes eXpress different is that it is an online (or streaming) algorithm, meaning it only makes one pass through the data. This allows it to be very light-weight and efficient using a constant amount of memory and time linear in the number of sequenced fragments be… posted by friends:  (1) @genetics_blog: Good talk by Lior Pachter at today’s #genomics seminar. Anxiously awaiting his #rstats pkg for dif exprssn w/ http://t.co/5SuXqESg0l counts 24.05.2013 22.59.53 posted by followers of the list:  (0) http://bit.ly/1aidUjd #rnomics_bioinfo

miRTCat: a comprehensive map of human and mouse micro#RNA target sites including non-canonical nucleation bulges

Summary: Micro#RNAs (#miRNAs) regulate various biological functions by binding hundreds of transcripts to impart post-transcriptional repression. Recently, by applying a transcriptome-wide experimental method for identifying #miRNA target sites (Ago HITS-CLIP), a novel non-canonical target site, named “nucleation bulge”, was discovered as widespread, functional and #evolutionally conserved. Although such non-canonical nucleation bulges have been proven to be predictive by using “pivot pairing rule” and sequence conservation, this approach has not been applied yet. To facilitate the functional studies of non-canonical #miRNA targets, we implement miRTCat: a comprehensive searchable map of #miRNA target sites including non-canonical nucleation bulges, not only mapped in experimentally verified #miRNA-bound regions but also predicted in all 3’ untranslated regions (3’UTRs) derived from human and mouse (~15.6% as expected false-positives).

Availability: http://ion.skku.edu/mirtcat

Contact: swchi@skku.edu

Supplementary information: Supplementary data are available at _Bioinformatics_ online. http://bit.ly/ZjPAxO #bioinformaticsj

viRome: an R package for the visualization and analysis of viral small #RNA sequence datasets

Summary: #RNA interference (#RNAi) is known to play an important part in defense against viruses in a range of species. Second-generation sequencing technologies allow us to assay these systems and the small #RNAs that play a key role with unprecedented depth. However, scientists need access to tools which can condense, analyse and display the resulting data. Here we present viRome, a package for R that takes aligned sequence data and produces a range of essential plots and reports.

Availability and implementation: viRome is released under the BSD license as a package for R available for both Windows and Linux http://virome.sf.net

Contact: mick.watson@roslin.ed.ac.uk

Supplementary information: Additional information and a tutorial is available on the ARK-Genomics website: http://www.ark-genomics.org/bioinformatics/virome http://bit.ly/ZjPAhy #bioinformaticsj

Structural #RNA alignment by multi-objective optimization

Motivation: The calculation of reliable alignments for structured #RNA is still considered as an open problem. One approach is the incorporation of secondary structure information into the optimization criteria by using a weighted sum of sequence and structure components as an objective function. As it is not clear how to choose the weighting parameters, we use multi-objective optimization to calculate a set of Pareto-optimal #RNA sequence-structure alignments. The solutions in this set then represent all possible trade-offs between the different objectives, independent of any previous weighting.

Results: We present a practical multi-objective dynamic programming algorithm, which is a new method for the calculation of the set of Pareto-optimal solutions to the pairwise #RNA sequence-structure alignment problem. In selected examples, we show the usefulness of this approach, and its advantages over state-of-the-art single-objective algorithms.

Availability and implementation: The source code of our software (ISO C++11) is freely available at http://sysbio.uni-ulm.de/?Software and is licensed under the GNU GPLv3.

Contact: hans.kestler@uni-ulm.de

Supplementary information: Supplementary data are available at _Bioinformatics_ online. http://bit.ly/1ahCQrj #bioinformaticsj

Comparative transcriptome analysis of small noncoding RNAs in different stages of Trypanosoma brucei [BIOINFORMATICS]

Deep-sequencing of the small RNAs in two life stages of parasitic protozoan _Trypanosoma brucei_ shows that the small RNAs can derive from various sources. Those generated from rRNAs and tRNAs are differentially expressed in the two life cycles studied. http://bit.ly/1ahilek #RNAJ

CPAT 1.2.1 - #RNA Coding Potential Assessment Tool

mybiosoftware.com - admin 200) && (this.width >= this.height) ? 200: true); max-height: 200px; height: expression((this.height > 200) && (this.height >= this.width) ? 200: true); border: none;’/> CPAT 1.2.1 :: DESCRIPTION CPAT (Coding Potential Assessment Tool) is a novel alignment-free method which rapidly recognizes coding and noncoding transcripts from a large pool of candidates. ::DEVELOPER Wei Li’s Computational Epigenomics Lab :: SCREENSHOTS N/A :: REQUIREMENTS Linux Python R package :: DOWNLOAD  CPAT :: MORE INFORMATION Citation: Nucleic Acids Res. 2013 Apr 1;41(6):e74. doi: 10.1093/nar/gkt006. Epub 2013 Jan 17. CPAT: Coding-Potential Assessment Tool using an alignment-free logi…  show all text posted by friends:  (1) @biosoftcn: CPAT 1.2.1 – #RNA Coding Potential Assessment Tool http://t.co/RDvrQvqcIs 24.05.2013 11.08.41 posted by followers of the list:  (0) http://bit.ly/1agG2mX #rnomics_bioinfo

RSeQC 2.3.6 - #RNA-seq Quality Control package

mybiosoftware.com posted by friends:  (1) @biosoftcn: RSeQC 2.3.6 – #RNA-seq Quality Control package http://t.co/f2uWcWD4lI 24.05.2013 10.42.39 posted by followers of the list:  (0) http://bit.ly/1agG2Dj #rnomics_bioinfo

Cenix Bioscience and Debiopharm collaborate to identify predictive biomarkers

Cenix BioScience a specialist in preclinical contract research and technology development in the field of ##RNAi #miRNA and high contentdriven pharmacology and Debiopharm Group Debiopharm a Switzerlandheadquartered global biopharmaceutical group of companies… http://bit.ly/ZjdHga #bioportfolio

Epigenetics and transgenerational inheritance

A report on the ‘Non-coding #RNA, epigenetics and transgenerational inheritance’ meeting, Churchill College, Cambridge, UK, 11-12 April 2013. http://bit.ly/ZiV2kF #BMC