Korilog News
Korilog at BioIT World Expo
Meet us at the BioIT World Conference and Expo that will take place April 29-May 1, 2014 in Boston MA, USA.

Come over our poster to discover the novelties coming with the new release of the KLAST sequence similarity search tool.
 
Genome Assembly & Analysis Toolbox

Inria's Genscale team has just released the Genome Assembly & Analysis Tool Box (GATB) to provide an easy way to develop efficient and fast NGS tools. GATB is a C++ library of high level functions designed to benefit from innovative data structures for handling huge datasets from sequencing machines.

The toolbox comes as a free open-source C++ library, as well as ready-to use softwares for various NGS applications: k-mer counter, assembler, scaffolder, variant detection.

Here is a use case showing the amazing efficiency of the GATB toolkit: the assembly of a complete genome on a Raspberry Pi micro-computer.

 
KoriScale Inria Innovation Lab

Korilog and Inria Rennes Bretagne Atlantique have setup KoriScale, an Inria Innovative Lab (iLab) in the field of bioinformatics. During the coming three years, the company will work with Inria's Genscale team to further improve the KLAST technology and create new high-performance algorithms to decypher next-generation sequencing data.

Read more about Inria Innovation Lab.

 
ngKLAST 4.3 now available

ngKLAST 4.3's major features:

  1. ngKLAST can handle query sizing up to 2 million sequences per single run with only 2 Gb of RAM;
  2. Project Manager Module: the Job Results viewer provides a convenient control to automatically bin queries having hits vs. queries that do not match any hits;
  3. Project Manager Module: the Biological Classification Overview panel (BCO Viewer) provides new tools to handle Taxonomy: display of rank, computation and analysis of Lowest Common Ancestors (LCA);
  4. A new biological classification data processing tool has been added to enable the comparison of KLAST results given a user-chosen classification;
  5. Databank Manager Module now supports the DNA barcoding sequence databanks available from BOLD;
  6. Databank Manager Module now enables the installation of personal release of biological classifications: NCBI Taxonomy, Gene Ontology, Enzyme, Pfam and InterPro;
  7. ngKLAST/KServer: a single user can now submit and execute simultaneously several jobs an a KServer;

Comparison of Taxonomy data Taxonomy LCA analysis
 ngKLAST Comparison tool  ngKLAST LCA tool

Read more about the release 4.3 of ngKLAST.

 
Korilog raises private fundings

Korilog today announced a seed funding to help the company bring to market the KLAST technology.

Fundings come from Logoden Participations and XMP-Grandes Ecoles business angels funds. Patrick Durand, founder and CEO of Korilog, is also very pleased to welcome Dominique Lavenier to the board of the company. M. Lavenier is the director of Inria/Genscale team and creator of the KLAST technology.

 
Meet Korilog at KNIME meeting
Meet us at the 7th KNIME User Group Meeting that will take place on February 12-14, 2014 in Technopark, Zurich, Switzerland.
 
Meet Korilog at Inria Industry Day

Meet us at the Inria Industry Day that will take place February 11th, 2014 in Lyon, France.

Korilog will exhibit the new release of ngKLAST (4.3), as well as KNIME and CLC bio KLAST-based plugins. Come over our booth to meet us, as well as Dominique Lavenier, head of Inria/Genscale team and creator of the KLAST technology.

 
CLC bio KLAST plugin major update

Korilog, today released a major update of the KLAST plugin for CLC Main and Genomics Workbenches. Among the new features, we can mention:

  • the availability of a Databank Manager, a graphical component to facilitate the installation of reference databanks from public and personal sources; accepted format are FASTA, Genbank, EMBL, Genpept, Uniprot, Silva and BOLD
  • the capability of the KLAST engine to introduce biological classification data within the KLAST results (GeneOntology, Enzyme, NCBI Taxonomy, etc.)

More is available on the CLC bio KLAST plugin page.

 
CLC bio and Korilog release KLAST plugin

CLC bio and Korilog release KLAST software plug-in for fast, accurate sequence similarity search in next-generation sequencing

  • The combination of KLAST with CLC bio’s market-leading bioinformatics platform accelerates sequence similarity search up to 25 times compared to current standard BLAST

  • CLC Genomics Workbench now comes with free issue of KLAST for four computer cores

Aarhus, Denmark, and Questembert, France -- January 10, 2014 - CLC bio, a QIAGEN company, today announced in collaboration with Korilog the release of the KLAST plug-in for CLC Genomics Workbench and CLC Main Workbench to accelerate the analysis of data from next-generation sequencing (NGS). KLAST is a new sequence similarity search tool which builds on a highly optimized implementation of the PLAST algorithm published in BMC Bioinformatics. KLAST is comparable to the current standard BLAST providing a similar accuracy, but can perform up to 25 times faster (with comparable search parameters and multicore threaded configuration). Another important KLAST benefit is that its algorithm is designed to compare two large sets of sequence databanks in a single run.

“The integration of the KLAST plug-in into CLC Genomics Workbench makes it possible to perform sequence similarity queries on very large data sizes, which adds significant utility to the very critical challenge in analyzing next-generation sequencing data,” said Mikael Flensborg, Director of Global Partner Relations for CLC bio. “This solution will allow users to significantly accelerate their research by providing them with this fast, accurate, and NGS-scalable sequence similarity search software that integrates with our CLC Genomics Workbench, and offers a very user-friendly graphical interface.”

“We are very enthusiastic to join forces with CLC bio’s market-leading bioinformatics platform,” said Patrick Durand, Founder and CEO of Korilog. “KLAST has been available for only a few months, and we have many researchers switching to use this new tool for their NGS applications. We’re looking forward to offering more options for all of our users, as well as the users of both CLC Genomics Workbench and CLC Main Workbench.”

The logic of KLAST is different from BLAST, and can provide significant accelerations of seed-based heuristic comparison methods using multi-threading and SSE instructions that make the tool high-performing and more scalable than BLAST on multiple cores.

January Bundle Campaign

Throughout January 2014, users purchasing a CLC Genomics Workbench license will receive the KLAST plug-in for four computer cores at no extra cost. For more information please visit: http://www.clcbio.com/link.php?id=631.

 

About Korilog

Korilog, a privately held company based in Questembert, France, is a bioinformatics company providing the next generation of graphical software to integrate and explore data on pathways, genomes and proteomes. The company provides academic and industry research labs with desktop and web-based software programs (ngKLAST) as well as expert software development services to support researchers in their R&D activities. For further information, please visit www.korilog.com.

About CLC bio

CLC bio, a QIAGEN company based in Aarhus, Denmark, was founded in 2005 and has created the leading commercial data analysis solutions and workbenches for next-generation sequencing (NGS). It serves leading research institutions and top pharmaceutical companies worldwide. CLC bio’s products are used as an integrating workbench to handle biological data generated by a sequencer through a series of analysis stages. CLC bio’s leading products are CLC Genomics Workbench, a comprehensive and user-friendly analysis package for analyzing, comparing and visualizing NGS data; and CLC Genomics Server, a flexible enterprise-level infrastructure and analysis backbone for NGS data analysis. For more information, please visit www.clcbio.com.

About QIAGEN

QIAGEN N.V. is a Netherlands holding company publicly traded on NASDAQ and Frankfurt Prime Standard. The Company is the leading global provider of Sample & Assay Technologies that are used to transform biological materials into valuable molecular insights. Sample technologies are used to isolate and process DNA, RNA and proteins from biological samples such as blood or tissue. Assay technologies are then used to make these isolated biomolecules visible and ready for interpretation. QIAGEN markets more than 500 products around the world, selling both consumable kits and automation systems to customers through four customer classes: Molecular Diagnostics (human healthcare), Applied Testing (forensics, veterinary testing and food safety), Pharma (pharmaceutical and biotechnology companies) and Academia (life sciences research). As of September 30, 2013, QIAGEN employed more than 4,100 people in over 35 locations worldwide. Further information can be found at www.qiagen.com.

Contacts:

CLC bio:
Lasse Görlitz, VP of Communications
Tel: +1 (617) 765 0687
Email: lgoerlitz // clcbio.com

Korilog:
Patrick Durand, CEO
Tel: +33 (960) 368 038
Email: pdurand // korilog.com

 
KLAST for human health research

The University Laboratory of Biodiversity and Microbial Ecology (LUBEM, EA3882) at the University of Western Brittany (UBO, Brest, France) and the company Korilog have started a joint R&D project funded by CRITT Santé Bretagne.

In this context, the KLAST high-performance sequence similarity tool will be used to decypher pyrosequencing data to study the microbial diversity of patients with cystic fibrosis.

 
KlastRunner 4.1 released

The new 4.1 version of the KlastRunner software comes with:

  1. the possibility to introduce Biological Classification data (NCBI Taxonomy, Gene Ontology, Enzyme and Interpro) within Klast results
  2. the possibility to reformat Biological Classification (BCO) data from standard KLAST tabular format (-outfmt 1) into a query-oriented report containing only BCO;
  3. a graphical editor to facilitate the creation of data filters;
  4. two new output formats: tabular Blast-like (-outfmt 2) and user-defined (-outfmt 3);
  5. a new KLAST engine, optimized for klastn comparisons. This new release is up to 5x faster than the previous klastn.

Please, have a look at the updated user manual for more information.

 
ngKLAST for DNA barcoding

Meet us at the Colloque de Génomique Environnementale that will take place November 4-6, 2013 in Rennes, France.

We will show the new ngKLAST features to run DNA barcoding analyses. And together with Inria, we will present KLAST applications during a Tech Track.

 
ngKLAST 4.2 now available

ngKLAST 4.2's major features:

  1. the Project Manager Module includes a Search Control allowing to search for text patterns within the Job Result table,
  2. you'll find also a highly improved [Export Queries] feature capable of exporting queries along with biological classification data (NCBI Taxonomy, Enzyme, GO) in various formats (Fasta and tabular),
  3. the Databank Manager Module enables the move of an entire repository from one HDD storage to another one,
  4. ngKLAST is shipped with an improved KLAST engine.

Search for taxonomy data within Result Table
 ngKLAST Search tool

Read more about the release 4.2 of ngKLAST.

 
Korilog's Innovation Award

Korilog is the winner of an Innovation Award (Trophée de l'Innovation) from CCI Morbihan. An award for the development of the KLAST high-performance sequence comparison technology by Korilog and Inria's Genscale Team.

 
Korilog at ISMB in Berlin
Meet us at the ISMB/ECCB annual meeting that will take place July 21-23, 2013 in Berlin, Germany.

Come over our exhibitor booth (#28) to discover the many NGS uses of our new, fast, accurate and scalable sequence similarity search tool: KLAST.
 
ngKLAST 4.1 now available
Tuesday, 02 April 2013 00:00

ngKLAST 4.1 introduces:

1. the management of Silva databank for rRNA analyses;

2. new features (such as sorting, query tree management) within the Project Manager and Search modules;

3. a full compatibility with the new KServer providing a powerfull client-server KLAST-based system.

Please read the full release note to have an overview of all the novelties of ngKLAST 4.1.

 
Genoscope Benchmarked KLAST on Tara Oceans Data

March 27th, 2013. Evry (France) - National Center for Sequencing / Genoscope / CEA has benchmarked KLAST on metagenomic data sets from the Tara Oceans International Research Project. This benchmark has been conducted by Thomas Vannier from the research team of Jean-Marc Aury on metagenomic sequences produced by the Sequencing Laboratory headed by Patrick Wincker.

The main goal of the test was to evaluate speedup and quality of results obtained by KLAST in comparison with BLAST, which is usually used at Genoscope to run sequence comparisons. Quality was evaluated in two ways. First, crude results from both tools were compared, i.e. how much results from BLAST are also found by KLAST. Second, by using results from both tools to assign each query to a taxonomy entry.

KLAST achieved sequence comparisons 12x to 18x times faster than BLAST, while covering up to 96% of the results produced by BLAST.

This benchmark illustrates the benefits of using KLAST both in terms of quality results and speed on the decyphering of Tara Oceans metagenomic data.

Read more about the benchmark.

 
Korilog at Gen2Bio 2013
Meet us at the Gen2Bio meeting that will take place on March, 28th 2013 in Nantes, France. We will show the use of the coming 4.1 release of ngKLAST.
 
Announcing ngKLAST

Korilog announces the release of ngKLAST, the brand new release of KoriBlast including the KLAST high-performance sequence similarity search tool. With an easy-to-use workflow engine and a unified set of data viewers, the ngKLAST platform makes large scale databanks exploration accessible to every life science researcher. Discover the new software platform:

Read more about the ngKLAST software.

 
KLAST now available

KLAST has been released. The new high-performance sequence similarity search tool developped by Korilog and Inria is now available as an Extension for KNIME.

KLAST for KoriBlast soon to be available... stay in touch.

 
KoriBlast 3.4 now available

KoriBlast 3.4 introduces:

1. a new Biological Classification Overview viewer enabling the global analysis of annotated hits. The viewer is designed to get a general overview of functional (Enzyme, GeneOntology, InterPro) and taxonomy content of NGS data sets.

2. an enhanced data management system to handle the analysis of larger set of sequences.

Biological Classification Overview
 Biological Classification Overview

Please read the full release note to have an overview of all the novelties of KoriBlast 3.4.

 
Korilog at ECCB 2012
Meet us at the ECCB annual meeting that will take place 9-12 September 2012 in Basel, Switzerland.

Come over our booth to discover the many NGS uses of our new, fast, accurate and scalable sequence similarity search tool: KLAST.
 
Announcing KLAST - High-performance Sequence Similarity Search Tool

Korilog and Inria announce collaboration on significant acceleration of BLAST

Questembert, France, June 15th, 2012 - Korilog and Inria today announced the integration of the PLAST technology into Korilog software platforms. Licensed by Korilog from Inria, PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of the Blast suite of algorithms.

Korilog and the Inria Genscale’s team collaborated closely on a eighteen-month R&D project to create KLAST, a new optimized implementation of the PLAST algorithm recently published in BMC Bioinformatics.

Korilog "A key issue in searching for similarities between sequence databanks is dramatically reducing execution time, while keeping a high quality in the resulting data. KLAST not only meet these two goals but its innovative implementation takes into account the exisiting IT infrastructure of many labs. Indeed, KLAST achieves accelerations without the need of any additional hardware devices, but it takes full advantage of multi-core processors available in common desktop computers or cluster nodes. We are very excited to provide our users with such an elegant tool", states Patrick Durand, CEO at Korilog.
KLASTp benchmarks using the black cottonwood Populus trichocarpa species have demonstrated a 24x increase in speed using KLAST software accelerator compared to BLAST, both tools ran on 8 cores of an Apple MacPro computer. This benchmark used KLASTp to compare 2,327 proteins against 2.9 million proteins from the NCBI RefSeq databank. Compared to BLAST and SSearch, KLAST is as sensitive and selective as these reference tools. Equivalent accelerations and quality are achieved with the other KLAST comparison tools, KLASTx, tKLASTn, tKLASTx and KLASTn. KLAST vs. BLAST performance
Inria Dominique Lavenier, PLAST scientific leader, notes: "The transfer of PLAST into a Hi-Tech company like Korilog is a very gratifying and important step for our research team. It allows us to directly contribute to new advances in emerging biological fields, from health and disease to agriculture and environment. And feedback from end-users is highly valuable to keeping PLAST as a technology leader in intensive sequence comparison." .

The KLAST sequence similarity search engine provides the following features:

  • support for all types of sequence comparisons
  • handle all lengths of sequences
  • direct support of sequence files, without the need to pre-built static sequence indexes
  • integrate a data filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.)
  • NGS scalable

To provide users with an advanced sequence similarity search platform, the KLAST engine has been integrated in the Korilog Bioinformatics Extensions for KNIME. As a result, users benefit from Korilog plugin’s features and from a wide rande of data analysis methods coming with the KNIME platform. KLAST is available for the various releases of KNIME, from Desktop up to Cluster Execution. Command-line execution is also available.

"The integration of KLAST within the KNIME platform provides researchers with a very versatile genomics data analysis platform combining KNIME's extended data analysis nodes with the fast sequence similarity search engine created by Inria and Korilog. Using KLAST within KNIME will enable convenient sequence similarity results analysis, such as statistics, data filtering, data comparison, biological classification overview and interactive views", comments Michael Berthold, CEO at KNIME.AG. KNIME

Other enhancements are underway to speedup KLAST even more.

The KLAST project is part of the KoriPlast Collaborative Research program conducted by Korilog, financed by the Brittany Region and accompanied by CRITT Santé Bretagne.

During Summer and Fall 2012, Korilog will release new versions of its Bioinformatics Plugin for KNIME, KoriBlast and KoriBlast Server integrating the new high-performance KLAST search tool.

Stay in touch by following us on Twitter.

 

About Korilog

Korilog is a bioinformatics company providing next generation of graphical softwares to integrate and explore pathways, genomes and proteomes data. The company provides academic and industry research labs with desktop and web-based softwares (KoriBlast, KoriViewer) as well as expert software development services to support researchers in their R&D activities.

About Inria

Working at the crossroads of computer sciences and mathematics, over the last 40 years Inria’s researchers have been developing the scientific foundations for a new field of learning: computational sciences. When associated with other scientific disciplines, computational sciences can be used to offer new concepts, languages, methods and teaching aids which open up new avenues for exploration and understanding of complex phenomena. Working in project-teams, Inria researchers mix fundamental and applied research in an innovative blend to produce their results. The institute’s 174 teams, the majority of which are joint teams with other major French or international research bodies, are comprised of around twenty researchers working on a shared project for a period of 4 to 8 years. Inria is France’s only public research body fully dedicated to computational sciences. It hosts over 1000 young researchers each year.

 
Korilog at Jobim 2012
Meet us at the Jobim annual meeting that will take place 3-6 July 2012 in Rennes, France.

Come over our booth to preview a new, fast, accurate and NGS scalable sequence similarity search tool created by Inria and Korilog.
 
Korilog at ASM 2012
Meet us at the general meeting of the American Society for Microbiology (ASM) that will take place 16-19 June 2012 in San Francisco, USA.

Come over booth 1239 to preview a new, fast, accurate and NGS scalable sequence similarity search tool created by Inria and Korilog.
 
BlastViewer 2.4 now available

We have released a new version of our free BlastViewer. This is mainly a maintenance version where a few bugs have been fixed and some user-requested features have been added (such as the display of query ID within the Iteration selector). Download the new release here.

 
KoriBlast 3.3 now available

KoriBlast 3.3 introduces:

1. a new Hit Reference Map Viewer enabling the analysis of queries matching a reference sequence,

2. a new Multiple Sequence Alignment Editor combined with a Distance Tree Viewer,

3. enhanced data exports where Blast annotations (e.g. biological classifications data) are saved within text and CSV reports,

4. the access to several new search parameters for Local Blast and KoriBlast Server search systems.

Hit Reference Map Viewer MSA Editor / Distance Tree
 Hit map Viewer - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems  MSA Editor - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems

 

KoriBlast Server 3.1 new features:

1. the administrator can now handle user access permissions on databanks,

2. KoriBlast is capable of maintaining up-to-date the list of sequence databanks available on the KoriBlast Server.

Read more in the full release note.

 
Korilog at Gen2Bio 2012
Meet us at the Gen2Bio meeting that will take place on March,29th 2012 in Lorient, France. We will show the use of the coming 3.3 release of KoriBlast.
 
Korilog at VIZBI 2012
Meet us at the Vizbi meeting (Visualizing Biological Data) that will take place 6-8 March 2012 at EMBL-Heidelberg, Germany. We will show the applications of KoriBlast for funtional metagenomics analysis.
 
Korilog at Knime User Meeting
Meet us at the Knime User Group meeting that will take place between January 30 and February 3, 2012 in Zurich, Switzerland.
 
KoriBlast 3.2 now available
Wednesday, 30 November 2011 15:00

KoriBlast 3.2 introduces:

1. a new Classification Viewer enabling the analysis of Taxonomy, GeneOntology, InterPro and Enzyme data within the Analysis Module.

2. an NGS-enhanced Global Analysis Module enabling the interactive exploration of 1,000,000+ annotated hits.

3. several user interface enhancements, such as the batch sequence editing feature (NGS applications).

Classification Viewer Global Analysis Module
 Classification Viewer - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems  Global Analysis Module - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems

 

This release of KoriBlast is also fully compliant with the new KoriBlast Data Server. Available as a separate product, this software enables the use of a dedicated computer infrastructure to run annotated Blast jobs. The server software is compatible with SGE/OGE and PBS jobs scheduling systems, and is capable of using the standard Blast as well as mpiBlast.

KoriBlast Server - Architecture
 KoriBlast Server - Architecture - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems

Please read the full release note to have an overview of all the novelties of KoriBlast 3.2.

 
Korilog releases a bioinformatics extension for Knime

Korilog releases a bioinformatics extension for KNIME

The open-source KNIME platform, from the University of Konstanz, is a widely-used graphical software enabling researchers to easily design data analysis workflows.

With the addition of the Korilog Bioinformatics Extension for Knime, it is now easy to setup and run databank exploration workflows directly within KNIME.

The Korilog Bioinformatics Extension for KNIME provides several additional nodes to the KNIME platform to handle large set of sequences and run sequence comparison workflows in multi-threaded batch mode. Data produced with such workflows can be annotated, filtered and provided to existing KNIME data handling nodes for further analysis and visualization. Read more.

Korilog is an official technology partner of KNIME.

 
KoriViewer on Genouest Blast server

KoriViewer now available on Genouest Blast server

Korilog has been chosen by the Genouest Bioinformatics platform to deploy KoriViewer, the web-based annotated Blast results visualization environment.

Read more... [KoriViewer on Genouest Blast server]
 
KoriBlast deployed at Ifremer

Korilog deploys its KoriBlast databank exploration solution at Ifremer

Korilog has been chosen by the French Research Institute for the exploitation of the sea (Ifremer) to deploy KoriBlast, the graphic sequence database exploration platform, to be used with the Institute's SGI super-calculator running MPI-Blast.

Read more... [KoriBlast deployed at Ifremer]
 
KoriBlast 3.1 now available

KoriBlast 3.1 introduces:

1. a new data management engine enabling the use of large sequence files and results (eg 300,000 annotated proteins or more).

2. a new HTML export feature providing a convenient way to share results with colleagues or clients.
Follow this link to view an online sample data set produced by KoriBlast.

3. several user interface enhancements, such as the Massive Sequence Editor. It enables researchers to easily copy, cut or edit a subset of sequences from a file containing well over 200,000 sequences and to obtain a rapid overview of the distribution of sequence size.

Massive Sequence Editor Share KoriBlast results with a web browser
Massive Sequence Editor - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems
HTML Export - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems

A new feature is available for users having the KoriBlast-PathwayExplorer software package: the direct exploration of metabolic pathways from EC-annotated Blast results.

Metabolic Pathway Analysis
Metabolic Pathway Analysis - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems
PathwayExplorer is developed by our partner, Genostar Bioinformatics


Read the release note for more information.

 
Meet us at Jobim 2011, Paris
Korilog will exhibit at Jobim 2011 that takes place in Pasteur Institute, Paris, France, on June 2011.
 
Korilog and INRIA research project

The Brittany Region gives its approval to launch the collaborative Korilog/INRIA research project, KoriPlast, for the development of a high-performance system for comparing genome sequence databases.

Read more... [Korilog and INRIA research project]
 
LabCollector and KoriViewer for Blast analysis in a LIMS

Korilog announces the integration of its web application KoriViewer within AgileBio's LabCollector LIMS. KoriViewer extends LabCollector' Sequence Module, enabling researchers to conduct extended exploration of Blast search results using an integrated, web capable, sequence management solution.

Read more... [LabCollector and KoriViewer for Blast analysis in a LIMS]
 
KoriBlast 3.0: a major update

KoriBlast 3.0

In this new release, the following major features have been added:

1. Use the Global Analyse Module to browse interactively very large sets of fully annotated hits using biological classifications, such as NCBI Taxonomy, Gene Ontology, Enzyme Commission and InterPro domains (up to 250,000 hits can be studied at once with 1 Go Ram).
2. Use the Databank Manager Module to automatically install public and personal databanks (Blast, annotations and biological classifications). Creation of taxonomic databank subsets is also possible.
3. Use the redesigned Search Module to run new powerful features, such as global filtering and data retrieval to be applied on existing results.
4. Prepare directly functionaly annotated Blast results. Blast job results can be annotated with the following biological classifications: NCBI Taxonomy, Gene Ontology, Enzyme Commission, InterPro and Pfam domains.

Read more in the complete release note. Read the KoriBlast 3.0 product page.

 Global Viewer - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems  Databank Manager - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems
 
Meet us at ECCB 2010, Ghent
Korilog will exhibit at ECCB 2010 that takes place in Ghent, Belgium, on September 26-29, 2010.
 
Meet us at EED 2010, Paris (France)
As a sponsor of the third conference of the European Society for Evolutionary Developmental Biology (EED), Korilog will exhibit its bioinformatics solutions. The conference will be held in Paris (France), from 6 to 9 of July 2010. More.
 
New Powerful Pathway Exploration Tool

Korilog announces the integration of KoriBlast within Genostar's Metabolic Pathway Builder bioinformatics platform. Korilog's databank exploration software extends Metabolic Pathway Builder, enabling users to conduct large scale sequence studies bringing into play genomic, proteomic, transcriptomic and pathway data.

Metabolic Pathway Builder seamlessly integrates a suite of analytical methods and data for genomic, proteic and metabolic research, enabling users to perform comparative genomics, predict protein functions and enzymatic activity, and both explore and visualize metabolic pathways on multiple organisms of interest.

Koriblast is an easy to use, graphically-driven software module for global exploration of biological sequence databanks. It offers a unified access to remote and local sequence and data repositories. Users can take advantage of the multifunctional, configurable interface to design powerful search strategies combining batch sequence comparisons and to efficiently retrieve and filter their data. KoriBlast also features a set of comprehensive viewers to analyze search results, from sequences to 3D structures.

By integrating the software platforms, this partnership brings researchers a world-class, user friendly solution for analysis of NGS-generated sequences and expression data from genome to metabolome. Benefits include the ability to:

  • Efficiently and accurately annotate or reannotate genomic and proteic sequences, Map sequences on pathways
  • Identify and analyze syntenies and the metabolic reactions catalyzed by their gene products
  • Rapidly read, assemble and analyze data in all common formats, whether from complete chromosomes or large sets of newly sequenced cDNAs or contigs
  • Prepare and use personal sequence data repositories

The integrated platform enables a wide range of applications for public research institutes and agri-business, biotechnology and pharmaceutical industries:

  • Vaccine discovery and development
  • Animal health & nutrition
  • Diagnostics
  • Agro-foods
  • Cosmetics research
  • Infectious diseases

 

Use GenoAnnot and KoriBlast for automatic annotation transfer - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems

Use GenoAnnot and KoriBlast for
automatic annotation transfer

Map sequences to metabolism - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems

Map sequences to metabolism

About Genostar - www.genostar.com

Genostar is a bioinformatics company specializing in solutions for biological data analysis from genome to metabolome. Our software, data and expert services allow scientists to efficiently and visually interpret their sequence, expression and metabolic data, accelerating time-to-discovery. Genostar's strength in annotation and comparative analysis of multiple organisms contributes to infectious disease research, vaccine discovery, diagnostics and optimization of probiotics. Our integrated, flexible platform brings together a wide range of methods and data modeling, streamlining workflow, and making reporting and sharing of results fast and easy.

Contact: , COO. +33 476 971 070.


About Korilog - www.korilog.com

Korilog is a bioinformatics company providing academic and industry research laboratories with next generation software solutions in the key areas of data integration, exploration, management and visualization. Korilog provides ready-to-use graphical software (koriblast.com, koriviewer.com) enabling comprehensive exploration of sequence databanks and associated data. The company provides as well expert services to integrate specialized modules in Korilog' software, or create tailored tools and databanks to support researchers in their R&D activities.

Contact: , CEO. +33 960 368 038.

 
Meet us at Bio 2010, Chicago
Korilog will exhibit at Bio 2010 (booth 3712)  that takes place in Chicago, USA, on May 3-6 2010.
 
Meet us at Gen2Bio, St-Malo
Korilog will exhibit at Gen2Bio that takes place in Saint-Malo, France, on March 30, 2010.
 
KoriBlast 2.7 now available

KoriBlast 2.7

In this new release, the following features have been added:

1. Query NCBI major databanks and get sequences of interest using the Document Viewer's NCBI Entrez DataBase Explorer Tool. Sequence retrieval can be done interactively or in batch mode.
2. Export data in plain text files. Text format includes extended hit table and/or pairwise sequence alignments.
3. View protein sequences using the Hydrophobic Cluster Analysis (HCA) drawing system
4. Benefit from an extended display of summaries in the Search Module.
5. When creating local Blast databanks, KoriBlast now gets Fasta sequences out of these banks, instead of querying the NCBI.
6. For proteomics studies, KoriBlast computes theoretical pI and molecular weight.

Read more in the complete release note

 NCBI Entrez databases Explorer - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems
 
KoriViewer 3.0 now available

KoriViewer is a lightweight edition of KoriBlast providing the researchers with a full-featured graphical solution to analyse the results of in-house made Blast results.

From the researchers point of view, they will benefit from the complete Analyse module of KoriBlast.

From the IT administrators point of view, we are glad to provide them with a client-server based installation, enabling the deployment of KoriViewer within existing Blast search servers.

Read more.

 
Korilog softwares available in Japan
Korilog has signed an exclusive agreement with Ryoka Systems Inc. (RSI) for the reselling of Korilog' softwares. Under the agreement, RSI will sold the software to Japanese customers and will provide them with local support. Customers from Japan can check this page.
 
KoriBlast 2.6 now available

In this new release, the following features have been added:

1. PSI-Blast searches are available from the Search Module and the Analyse Module has been adapted to enable extended analysis of the results (see figure below, and view this video)
2. Prepare personal Blast databanks from native GenBank, Genpept, EMBL, SwissProt and Uniprot files, using either plain text or gzipped compressed files (view this video)
3. Install pre-formatted NCBI Blast databanks directly from their native 'tar.gz' files (view this video)
4. Design search filters enabling pattern matching on hit sequences
5. Compare search results to find new, common or deleted hits
6. Export KoriBlast data files and filters to share with colleagues having KoriBlast or BlastViewer
7. New Sequence Viewer to display and manipulate sequences (extract, translate, get compositions) downloaded from public repositories (see figure below)
8. Better handling of large projects involving thousands of sequences

Read more in the complete release note

kb compJobs  - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems kb docViewer  - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems


 
BlastViewer 2.3 now available

A new version of the KoriBlast Free Viewer (BlastViewer) has been released. The viewer better handles results containing numerous entries: multiple Blast outputs within a unique results file as well as PSI-Blast output files. It is capable of handling larger data files. As a consequence, the viewer now requires a minimum of 256Mo to start. BlastViewer is now able to read KoriBlast native data files, enabling the exchange of data with the KoriBlast platform. More.

 BlastViewer - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems
 
KoriBlast 2.5 now available

In this new release, two major tools have been added: a Project Manager and a Distance Tree viewer. The former enables the user to organize his/her search jobs using multi-level hierarchies. The latter provide the user with an integrated viewer aims at exploring distance trees created from query-anchored sequence alignments.

 search module big. - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems  analyse module big.p - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems

  Other new features include:

1. A new and more compact display of query-anchored alignments, including a Sequence Logo Viewer (Analyse Module)
2. New export formats for images, alignments and trees. Creation of PDF reports (Search and Analyse Modules).
3. The capability of analysing search results procuded by ScanPS (Analyse Module)

Read more

 
Korilog: a Young Innovative Company
Korilog has been labellized as Young Innovative Company by the French Ministère de la Recherche.
 
BlastViewer 2.2 now available
A new release of the KoriBlast Free Viewer (BlastViewer) has been released. It is now possible to export the hit table content to spreadsheet applications, to modify the graphical properties of the hit table (smilies and colours) and to fetch Blast results directly from the NCBI Blast servers. More.
 
KoriBlast 2.4 now available

In this new release, several user interface improvements have been added in the Search and Analyse Modules.

The Search Module runs a new job scheduler engine and is able to connect a Blast system managed by the Sun Grid Engine. This feature enables labs and companies to use KoriBlast for intensive sequence comparisons while using their own high-performance Blast search system.

During sequence data retrieval, KoriBlast now gets the various databank cross-reference identifiers (PubMed, KEGG, GO, InterPro, Enzyme, etc) that are available for the hit sequences reported in the sequence comparison results.

A new module has been added, namely the Document Viewer, to provide biologists with dedicated viewers to display complex data that does not fit within the Analyse Module frame. In this first release of the Document Viewer Module, KoriBlast provides a 3D structure viewer capable of displaying PDB entries.

 

analyse module big  - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems

 

Read more

 
KoriBlast for OUEST genopole

Korilog is announcing a new version of its KoriBlast software, adapted for using a calculation grid.

Aimed at biologists and bioanalysts, KoriBlast facilitates and accelerates sequence bank exploration. Offering a user-friendly graphic interface, closely combining methods of exploration, analysis, interrogation and viewing of sequence banks and associated data, KoriBlast makes access to these resources fully transparent, enabling scientists to focus on their analyses.

A partnership with the research facility INRIA Rennes - Bretagne Atlantique and the University Rennes I resulted in a system that enables the biologist to exploit a calculation grid to accelerate searches in sequence banks.

Installed on the bioinformatics services platform www.genouest.org , KoriBlast allows OUEST-genopole® users to access to the numerous sequence banks installed and regularly updated on the platform, by means of a proprietary calculation grid.

Laboratories connected to OUEST-genopole® with KoriBlast licenses can obtain a free update of KoriBlast from Korilog if they wish to use the genouest.org calculation grid.

Public research laboratories external to OUEST genopole® that have a BLAST system installed on a calculation grid or cluster can obtain KoriBlast with this new feature.

 

 
Two grants for Korilog
Korilog receives two grants from Oseo Innovation and the Conseil Général du Morbihan to start the development of a metagenomics release of KoriBlast.
 
Partnership with INRIA

Korilog and INRIA signs a partnership to develop a grid-capable release of KoriBlast.

A partnership with the research facility INRIA Rennes - Bretagne Atlantique and the University Rennes I has been started to enable biologists to exploit a calculation grid to accelerate searches in sequence banks.

In a first step, KoriBlast will be designed to exploit the calculation grid available on the bioinformatics services platform genouest.org from OUEST-genopole®. Laboratories connected to OUEST-genopole® with KoriBlast licenses will obtain a free update of KoriBlast if they wish to use the genouest.org calculation grid.

In a second step, public research laboratories external to OUEST genopole® that have a BLAST system installed on a calculation grid or cluster will be able to obtain KoriBlast with this new feature.

 
KoriBlast 2.3 now available
Among various improvements, KoriBlast is now capable of using a WWWBlast server, it provides a graphical interface to setup personal sequence databases and it is now possible to design search strategies combining sequence comparison, data retrieval and data filtering.
 
Korilog at EuroBIO 2007
EuroBIO 2007. Meet us at Lille, booth G20
 
KoriBlast 2.2 now available
Release of KoriBlast 2.2. The new release of KoriBlast provides the client to the EBI Blast server, a Taxonomy data viewer and a graphical configuration editor.
 
Two awards for Korilog
Korilog receives two awards from the Boutique de Gestion and the Fondation Jean Guyormac'h for its innovative software KoriBlast.
 
KoriBlast 2.1 now available
Release KoriBlast 2.1. This new release of KoriBlast provides more data export capabilities, a new Map viewer, the client to a Local Blast engine. KoriBlast is also Vista Ready.
 
KoriBlast 2.0
Korilog starts its business activities with the release of KoriBlast 2.0
 


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