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The Genome Analysis Centre | TGAC - NextClip

The Genome Analysis Centre | TGAC - NextClip | Bioinformatics and Lab Informatics Resources | Scoop.it
Sandrine Palcy's insight:

NextClip is a tool for comprehensive quality analysis and read preparation for Nextera long mate pair (LMP) libraries.

 

http://www.businessweekly.co.uk/biomedtech-/16342-new-bioinformatics-tool-for-complex-genome-analysis#!

Richard Leggett, at TGAC, said: “Regulating laboratory protocols and selection of sequenced data for downstream analysis are vital in making effective use of mate pair libraries.

“However, quality control of the libraries can require significant bioinformatics analysis. Further processing is also required to extract true mate pair reads, remove fragment junction adaptors and clip reads.

“For this reason we developed NextClip, a tool for comprehensive quality analysis of Nextera LMP libraries and preparation of reads for scaffolding.”

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Bioinformatics and Lab Informatics Resources
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antibodypedia

antibodypedia | Bioinformatics and Lab Informatics Resources | Scoop.it
Sandrine Palcy's insight:

Antibodypedia is an open-access database of publicly available antibodies against human protein targets. The site features user and provider data on antibody efficacy in a range of biochemical and cell biological techniques--so you can find the right antibody for the right application.

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Human Proteome Map

The Human Proteome Map (HPM) portal is an interactive resource to the scientific community by integrating the massive peptide sequencing result from the draft map of the human proteome project.
Sandrine Palcy's insight:

New draft map of the human proteome using high-resolution Fourier-transform mass spectrometry: Kim et al. A draft map of the human proteome. 2014. Nature.  509, 575-581 http://www.ncbi.nlm.nih.gov/pubmed/24870542

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The Human Protein Atlas

The Human Protein Atlas | Bioinformatics and Lab Informatics Resources | Scoop.it
Sandrine Palcy's insight:

The Swedish Human Protein Atlas project, funded by the Knut and Alice Wallenberg Foundation, has been set up to allow for a systematic exploration of the human proteome using Antibody-Based Proteomics. This is accomplished by combining high-throughput generation of affinity-purified antibodies with protein profiling in a multitude of tissues and cells assembled in tissue microarrays. Confocal microscopy analysis using human cell lines is performed for more detailed protein localization.

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Oxford Journals | Life Sciences | Nucleic Acids Research | Database Summary Paper Categories

Sandrine Palcy's insight:

The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases and recent updates to 123 databases previously featured in NAR or other journals.

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Virtual Ribosome

Sandrine Palcy's insight:

The Virtual Ribosome is a comprehensive tool for translating DNA sequences (in FASTA, GenBank or TAB format) to the corresponding peptide sequences.

 

Reference: Rasmus Wernersson.
Virtual Ribosome - a comprehensive DNA translation tool with support for integration of sequence feature annotation
Nucl. Acids Res. 2006 34: W385-W388

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MisPred (7.0)

MisPred (7.0) | Bioinformatics and Lab Informatics Resources | Scoop.it

The MisPred database is a collection of protein sequences identified by the MisPred pipeline as erroneous (incomplete, abnormal or mispredicted). The MisPred database may be searched in various ways and you may also analyze your sequence using the MisPred pipeline to decide whether your sequence violates some basic rules of protein sequences.

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bioDBnet - Biological Database Network

bioDBnet is a comprehensive resource of most of the biological databases available from different sites like NCBI, Uniprot, EMBL, Ensembl, Affymetrix.
Sandrine Palcy's insight:

bioDBnet is an online web resource that provides interconnected access to many types of biological databases.

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Rescooped by Sandrine Palcy from Modern Biology: of computers and men
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An analysis of a ‘community-driven’ reconstruction of the human metabolic network - Springer

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Sandrine Palcy's curator insight, July 18, 2013 5:40 AM

Review of human metabolic network Recon 2: a knowledgebase and a predictive model.

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Largest cancer database launched

Largest cancer database launched | Bioinformatics and Lab Informatics Resources | Scoop.it
The world's largest database of cancer patients is being set up in England in an attempt to revolutionise care, Public Health England has announced.
Sandrine Palcy's insight:

UK at the forefront of personalized medicine.

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The Open Biological and Biomedical Ontologies

Open Biological and Biomedical Ontologies,
a collection of freely available well-structured
controlled vocabularies.
Sandrine Palcy's insight:

The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. The groups developing ontologies who have expressed an interest in this goal are listed below, followed by other relevant efforts in this domain.

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Whole Genome rVISTA Submission page

Whole Genome rVISTA Submission page | Bioinformatics and Lab Informatics Resources | Scoop.it
Sandrine Palcy's insight:

WGRV enables users to query databases containing pre-computed genome coordinates of evolutionarily conserved transcription factor binding sites in the proximal promoters (from 100 bp up to 5kb upstream) of human, mouse and Drosophila genomes. TF binding sites are based on position weight matrices from the TRANSFAC Professional database. For a given set of coregulated genes WGRV returns statistically enriched and evolutionarily conserved binding sites, mapped by the rVISTA (Regulatory VISTA) algorithm. Users can then retrieve a list of genes from the query set containing the enriched TF binding sites and their location in the query set promoters.

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geneXplain platform | GeneXplain

geneXplain platform | GeneXplain | Bioinformatics and Lab Informatics Resources | Scoop.it
The geneXplain platform is an online toolbox and workflow management system for bioinformatics and systems biology. The individual modules, or Bricks, can be flexibly put together to workflows.
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compomics-sigpep - predicting peptide signatures for targeted proteomics - Google Project Hosting

compomics-sigpep - predicting peptide signatures for targeted proteomics - Google Project Hosting | Bioinformatics and Lab Informatics Resources | Scoop.it

A new software platform called Sigpep that analyses transition redundancy in selected reaction monitoring (SRM) assays. Building on this platform, we also created a web application to generate transition sets with unique signatures for targeted peptides.

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EpiC: Antigenicity And Functional Prediction

EpiC: Antigenicity And Functional Prediction | Bioinformatics and Lab Informatics Resources | Scoop.it
EpiC, a tool to aid researchers in the selection of epitope
for affinity proteomics. Meta-server for prediction of antigenicity.
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Korilog News

Korilog provides high-performance bioinformatics softwares to analyse genetics, genomics, metagenomics and next-generation sequencing data (NGS).
Sandrine Palcy's insight:

Free Release of KLAST

A Free version of KLAST for the command-line (KlastRunner) is available at no charge for users from academic and non-profit institutions. The Free version enables KLAST for the command-line to use 4 core computers to compare up to 4 Gb of sequence data per job. This version meets the needs of most users.

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Call for data analysis papers : Nature Genetics : Nature Publishing Group

Call for data analysis papers : Nature Genetics : Nature Publishing Group | Bioinformatics and Lab Informatics Resources | Scoop.it
Community standards for data access, interoperability and metadata only make sense if data are creatively reused to further research. We are therefore inviting the submission of Analysis papers that reformat and integrate existing data sets to generate substantial novel insights into gene expression in cell differentiation transitions and different cell fates.
Sandrine Palcy's insight:

Innovation in scientific data publication: Let's see where it goes...

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The Genome Analysis Centre | TGAC - NextClip

The Genome Analysis Centre | TGAC - NextClip | Bioinformatics and Lab Informatics Resources | Scoop.it
Sandrine Palcy's insight:

NextClip is a tool for comprehensive quality analysis and read preparation for Nextera long mate pair (LMP) libraries.

 

http://www.businessweekly.co.uk/biomedtech-/16342-new-bioinformatics-tool-for-complex-genome-analysis#!

Richard Leggett, at TGAC, said: “Regulating laboratory protocols and selection of sequenced data for downstream analysis are vital in making effective use of mate pair libraries.

“However, quality control of the libraries can require significant bioinformatics analysis. Further processing is also required to extract true mate pair reads, remove fragment junction adaptors and clip reads.

“For this reason we developed NextClip, a tool for comprehensive quality analysis of Nextera LMP libraries and preparation of reads for scaffolding.”

more...
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DGIdb - Mining the Druggable Genome

DGIdb, The Drug Gene Interaction Database, is a research resource that can be used to search candidate genes against the known and potentially druggable genome.
Sandrine Palcy's insight:

A searchable online database of drug-gene associations.

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The Elements of Bioinformatics | Eagle Genomics

The Elements of Bioinformatics | Eagle Genomics | Bioinformatics and Lab Informatics Resources | Scoop.it
Sandrine Palcy's insight:

An interactive table for genomes and DNA-sequence oriented tools.

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Recon x

Recon x | Bioinformatics and Lab Informatics Resources | Scoop.it
Sandrine Palcy's insight:

Recon 2: a consensus biochemical knowledge-base on human metabolism

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2013/06/07 > BE Etats-Unis 334 > Séquençage de l'ADN - Partie 1 : Les grands enjeux industriels des nouvelles technologies aux Etats-Unis

2013/06/07 > BE Etats-Unis 334 > Séquençage de l'ADN - Partie 1 : Les grands enjeux industriels des nouvelles technologies aux Etats-Unis | Bioinformatics and Lab Informatics Resources | Scoop.it
Les Bulletins Electroniques des Ambassades de France - un service ADIT
Sandrine Palcy's insight:

Faisons le point!

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SilVA: Silent Variant Analysis using random forests — Computational Biology Lab, University of Toronto

SilVA: Silent Variant Analysis using random forests — Computational Biology Lab, University of Toronto | Bioinformatics and Lab Informatics Resources | Scoop.it
Sandrine Palcy's insight:

Automated harmfulness prediction of synonymous (silent) mutations within the human genome.

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Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization

Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization | Bioinformatics and Lab Informatics Resources | Scoop.it

Network Data Integration, Analysis, and Visualization in a Box

 

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

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Genome-wide analysis of long noncoding RNA stability

The first genome-wide map of RNA stability, with an emphasis in trying to understand long noncoding RNAs.

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