Intrepid Bioinformatics Software

Intrepid Bioinformatics offers a solution to help you with your data management needs when it comes to genetic data. Whether NGS data in BAM or FastQ format or SNP Chip data in .ab1, .vcf, or other similar formats, your data is secured by our Oracle® database and ready to visualize and analyze. It can be made visible only to you or shared with parties of your choice. You can even choose to publicize your data if you wish!

Our open API allows you to have full programmatic control over your data, essentially treating the database like one large file system. With minimal work, you can write your own analysis software or alter your current software and statistical packages to integrate with your data on our servers. No need to mess with data stored in multiple locations on various hard drives or servers.

NGS data:
Intrepid Bioinformatics is proud to announce the release of its new service supporting Next Generation Sequencing (NGS) data (run on Oracle Database 11gR2 and Linux 5.5). This new service is designed to improve how you interact with your NGS data, ensuring a safe, secure environment in which you can freely access and collaborate on your data.

When you send us your BAM or FastQ files, we make them available only to you on our Oracle® database and, if you choose, available to colleagues or even the public. We have enhanced the Integrative Genomics Viewer (IGV) to utilize our database, allowing you to quickly access your data without having to download large files over and over again or ship around cumbersome hard drives. If you wish to go beyond visualization with the IGV, you can use our open API to plug in your current analysis tools or design new ones from scratch. Our web services are designed to act like a file system allowing you to query directly, so we do not get between you and your data.

SNP and Genotype Data:
Our service is designed to improve how you interact with your data so that you can visualize it, perform your own analyses, and share data with collaborators, clients or even with the public.


When you send us your SNP data, we can map it to known genomes and make it immediately available for visualization. Our gene browser allows you to examine your data all the way down to the Sanger traces. You can view polymorphisms, exons and introns, allele frequencies, and more. Further, our open API allows you programmatic access to your data in a quick and easy manner akin to a file system on your computer so that you can design your own analyses and modify any tools and software you have to work with your data on our servers.

Software Link:  Intrepid Bioinformatics Software

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Bioinformatics analysis Software - Omixon Letter Space Toolkit

The Omixon Letter Space Toolkit is a suite of tools for performing bioinformatics analysis. The main tool is a gapped read mapper and alignment tool called ORM. The toolkit also contains a number of utilities for reformatting, sorting, filtering and parsing bioinformatics data, and handling very large files across a number of platforms.

The current version of Omixon Letter Space Toolkit is the first commercial version. A request for an evaluation downloaded can be made directly from this page.

The Toolkit allows mapping of reads from the Illumina, Roche 454 and Ion Torrent platforms. In theory, it should also be able to map letter space reads from the Life Technologies 5500 platform.

Note that we have two toolkits, there is also an Omixon Color Space Toolkit, which is for mapping and aligning color space data produced by Life Technologies series 4 (SOLiD) sequencers.

Command line Letter Space Toolkit
The main tools of the Omixon Letter Space Toolkit are available as a standalone Java application, which can be run from the command line. These tools automate the analysis, as well as automatically run it in parallel (if multiple processors are available).

The command line Toolkit comes with some supporting scripts, plus a comprehensive readme file that describes how to run the tools. An evaluation version of The Letter Space toolkit can be downloaded and tried for free.

Letter Space Toolkit features
The Toolkit includes highly accurate tools for detecting micro indels, SNPs and MNPs.

It offers a solution to map letter reads with a moderate distance (up to 30% sequence divergence) from reference genomes. It poses no restrictions on the size of the reference, which, combined with its high sensitivity, makes the Letter Space Toolkit well-suited for targetted sequencing projects and diagnostics.

The ORM tool within the Letter Space Toolkit is also extremely fast, and offers 'variable density indexing', where regions of greater interest (such as the exome) can be indexed more densely to improve sensitivity in those areas.

User Benefits
• Mapping of reads from the Illumina, Roche 454 and Ion Torrent platforms
• Finds larger indels than any other tool
• Performance is linear in respect to edit distance
• Very simple to run
• Choice of pre-set 'profiles' for species, platform and speed

Innovative Alignment
The Letter Space Toolkit contains sequencer-specific algorithms, settings and error correction models.

The main module of the Letter Space Toolkit - called ORM - follows the seed-and-extend paradigm. Letter space (base space) reads are indexed by ORM using spaced seeds and approximately mapped to a reference sequence database. ORM uses a second, much smaller seed to help to filter the approximate mappings. The underlying data structures are extremely economical for memory use, yet still provide high flexibility for trade-offs between sensitivity and specificity.

The fine alignment uses a combination of information and algorithms to produce its results, including the quality scores from the sequencer and a DNA mutation model. There are two main alignment techniques, a 'bridging' technique for smaller reads (such as Illumina short reads) where only one indel is expected, and a 'lacing' technique which allows for more indels per read, to cater for the longer Ion Torrent and Roche 454 reads.

Software Link:  Bioinformatics analysis Software - Omixon Letter Space Toolkit

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Bioinformatics analysis Software - Omixon Color Space Toolkit

The Omixon Color Space Toolkit is a suite of tools for performing bioinformatics analysis. The two main tools are a SOLiD gapped read mapper called Crema, and a statistical SOLiD fine aligner called AMAP. The toolkit also contains a number of utilities for reformatting, sorting, filtering and parsing bioinformatics data, and handling very large files across a number of platforms.

Note that the Omixon Color Space Toolkit used to be called the 'Omixon Variant Toolkit', but now that we have two separate toolkits we have renamed it. The new toolkit is the Omixon Letter Space Toolkit, which is for mapping and aligning 'letter space' (or 'base space') data produced by Illumina, Ion Torrent or Roche 454 sequencers.

Command line Color Space Toolkit
The main tools of the Omixon Color Space Toolkit are available as a standalone Java application, which can be run from the command line. These tools automate a number of analysis steps, as well as automatically run them in parallel (if multiple processors are available). The tools also manage their own memory consumption, so there is no special memory configuration required.

The command line Toolkit comes with some supporting scripts, plus a comprehensive readme file that describes how to run the tools. It can be tried for free for evaluation purposes - there's a 14 day evaluation license available. Please contact us for a quote for purchasing the command line Toolkit.

Color Space Toolkit features
The Toolkit includes highly accurate tools for detecting micro indels, SNPs and MNPs.

It offers a solution to map color reads with a moderate distance (up to 30% sequence divergence) from reference genomes. It poses no restrictions on the size of the reference, which, combined with its high sensitivity, makes the Color Space Toolkit well-suited for targetted sequencing projects and diagnostics.

The Toolkit also offers another unique feature - a fine alignment tool that takes the read quality scores into account using a well-defined probablistic model, plus integrates a choice of DNA mutation models. This leads to a significantly improved variant calling accuracy.

User Benefits
• Gives you the best chance to find the structural variation you are looking for
• Finds variants missed by all other techniques
• Maps more reads and thus provides the highest coverage
• Reports calculated structural variations with statistical significance
• Very simple to run
• Intuitive parameters

Bioinformatics features
• Choice of three pre-set sensitivity settings for mapping, plus option to use custom settings
• Choice of two fine alignment modes using different mutation models (one for coding regions, one for general DNA analysis)
• Automatic handling of lower quality bases without dismissing entire short reads or trimming.
• No need to run pre-filtering tools. Automatic recalibration of quality scores is part of the alignment.
• Allows any fasta or multifasta to be used as the reference (i.e. genomes and exomes supported)
• Runs the mapping and alignment steps together (with an option to run each alone)
• Choice of three strategies for mapping non-specific reads (read that map to multiple locations)
• Two quality filters available, for automatically screening out very low quality alignments
• Only a few parameters, with sensible defaults

File handling features
• Option to keep the rough mapping output as well as final finely aligned output
• Input in .fastq format, utilities provided to convert other formats to .fastq
• Output in standard .sam format, compatible with samtools
• Option to write out unmapped reads in .fastq format

Technical features
• If multiple processors are available the toolkit will automatically split the input and run in parallel
• Memory is managed without any user intervention
• Simple and flexible configuration
• Simple installation
• Comes with instructions and sample configurations

Innovative Alignment
The Color Space Toolkit was designed and written from the ground up to work with SOLiD data.

The mapping module of the Color Space Toolkit - called Crema - follows the seed-and-extend paradigm underlying successful tools such as BLAST and SHRiMP. Color reads are indexed by Crema using spaced seeds (or so-called neighbor seeds) and approximately mapped to a reference sequence database. The underlying data structures are extremely economical for memory use, yet still provide high flexibility for trade-offs between sensitivity and specificity. Crema has an innovative indexing technique and maps more reads than SHRiMP or BFAST at comparable trade-off settings.

The fine alignment module of the Color Space Toolkit - called AMAP - uses a combination of information and algorithms to produce its results, including the quality scores from the sequencer. AMAP has two modes, a nucleotide mode (using a DNA mutation model) and a codon mode (using a protein mutation model). The codon mode is only suitable for analysing coding regions, and is offered as part of our Human Exome online analysis service.

Software Link:  Bioinformatics analysis Software - Omixon Color Space Toolkit

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Kodon - Sequence analysis software

In an era of total genome research and growing bioinformatics needs, Kodon embodies a new generation of desktop based sequence analysis software.

Running on industry leading database engines such as Oracle® and Microsoft® SQL ServerTM, Kodon is capable of handling extremely large databases, and can analyze full chromosomes or genomes with unparalleled power and speed. Every feature is designed for use in genome sequencing projects of any size.

Fully integrated environment for sequence analysis, including megabase assembly, vector cloning, ligation, primer design, alignment, homology search, match and repeat analysis, structure analysis, and much more
GenBank and EMBL are Kodon 's native formats. No conversion, no loss of features and qualifiers from documented sequences.
Storage and full analysis capability on local computers. No need to upload data over the Internet, avoiding network traffic, enhancing data security.
Automatic updates of databases from public servers; integrated BLAST, sequence download, Medline search etc.
Powerful chromosome comparison and gene annotation tools

Software Link: Kodon - Sequence analysis software

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Canvas - Cheminformatics Software

Canvas is a powerful suite of cheminformatics tools built on innovative technologies that achieve unmatched performance and versatility. Canvas offers solutions to a wide range of problems faced by researchers with all levels of modeling expertise.

Details
The discovery of novel therapeutic agents requires exploring increasingly expanded and complex chemical space, resulting in rapidly growing data proliferation. Computational techniques that scale favorably with the expanding chemical space and provide efficient insights have become critical to any lead discovery and lead optimization effort.

Cheminformatics techniques such as fingerprint-based similarity searching and substructure matching can screen millions of compounds in seconds; clustering and diversity selection can analyze and improve the content of real and virtual compound libraries; principal components analysis and self-organizing maps reduce complex, high dimensional information into easily visualized relationships in a small number of dimensions; and supervised learning techniques offer quantitative models that elucidate structure-activity relationships and provide insights into new compounds' activities.

Software link: Canvas - Cheminformatics Software

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CLC Bioinformatics Database

CLC Bioinformatics Database is a smart and efficient way of managing sequence data in a 3-tier client/server architecture: a server containing one or more databases coupled with CLC workbenches as clients.

Components of the solution
• A database management system of choice; Microsoft SQL Server, Oracle, PostgreSQL, or MySQL.
• CLC Workbenches (clients) for interacting with the database.
• Thin client for administration and setup. -Upload and download of data.
• CLC Database Middleware to ensure scalability and performance.

Centralized sequence data management
In many bioinformatics organizations, the data is a virtual mess, since data is spread out on several computers in various formats and versions. Even employees' personal computers contain essential company data. The main advantages of the CLC Bioinformatics Database is centralization of data, storage, and management. Centralized data in combination with restricted user access makes it possible to be in control of the data and to share information in different groups across the organization. Centralized management of sequence data has been proven vital to increase the general knowledge level in an organization and increase productivity

Software Link:  CLC Bioinformatics Database

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Geneious Pro - Bioinformatics software

Geneious Pro is a revolutionary bioinformatics software platform that is both ultra-powerful and easy to use. Scientists, researchers and students are able to search, organize and analyze genomic and protein information via a single desktop program that provides publication ready images to enhance the impact of your research.

Details
Geneious Pro™ is an integrated and extendable software platform for the organization and analysis of biological data that runs on all major operating systems. Geneious Pro is a revolutionary bioinformatic tool that combines industry-leading DNA and protein analysis tools into a single package that is both ultra-powerful and easy to use. Scientists, researchers and students are able to search, organize and analyze genomic and protein information of any size via a single powerful desktop program that provides publication-ready images to enhance the impact of your research.

Software Link : Geneious Pro - Bioinformatics software

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RAPTOR - Protein Structure Prediction Software

RAPTOR is an innovative software tool designed for accurate protein structure prediction. It combines advanced analysis tools in one integrated software solution and provides three different threading methods.

Structure-based drug design approaches have been an integral part of the drug discovery process and have made a profound contribution at many pharmaceutical companies. As more and more structural information becomes available, a variety of practical structure-based techniques have been developed to accelerate the development at all stages of the drug discovery process. In spite of that, structure-based drug design requires a significant amount of structural resources from experimental methods. The recent explosion in genomic data has resulted in millions of protein sequences and researchers cannot afford to perform XRAY or NMR analysis on every protein. Currently, only 40 000 structures are stored in the PDB database. Consequently, pharmaceutical companies are increasingly turning to bioinformatics technologies which can reduce drug discovery and development costs. The practical role of protein structure prediction is now more important than ever.

Given a target protein sequence, if there is a homologous protein with known 3D structure, it can be found by using sequence search tools like PSI-BLAST or BLASTP. The target's structure is then built from the known structure. However, when the sequence homology is not significant, i.e. less than 25%, PSI-BLAST and BLASTP can not come up with a confident hit. Unlike PSI-BLAST or BLASTP, which simply does a sequence search, protein threading (fold recognition) makes use of both homology and structure information. It scans the protein sequence with an unknown structure against a database of known structures. By using a scoring function and conducting compatibility analysis between three-dimensional structures and linear protein sequences, the best structural template will be identified from which to build the sequence's structure. As a result, protein threading gives a superior prediction than homology modeling when there is marginal sequence homology. A comparison between RAPTOR and PSI-BLAST in CASP competitions can be found here.

RAPTOR is an innovative software tool designed for accurate protein structure prediction. It combines advanced analysis tools in one integrated software solution and provides three different threading methods. RAPTOR's unique integer programming optimization approach is most effective for finding structure templates of targets with low sequence homology and is able to generate high quality models. The easy-to-use interface and easy-to-understand E values are ideal for beginners and experts. Above all, the intuitive display of the output enables users to understand the results simply at a glance.

Software Link: RAPTOR -  Protein Structure Prediction Software

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BioNumerics - Bioinformatics software

BioNumerics is the only software platform to offer integrated analysis of all major applications in Bioinformatics: 1D electrophoresis gels, all kinds of chromatographic and spectrometric profiles, 2D protein gels, phenotype characters, microarrays, and sequences. The unique power of BioNumerics lies in its ability to combine information from various genomic and phenotypic sources into one global database and conduct conclusive analyses.

BioNumerics runs on industry leading database engines such as Oracle® and Microsoft® SQL ServerTM. With its integrated networking and client-server features, the software is the perfect backbone for universal data management and analysis within and between laboratories of any size.

• Unparalleled 1D gel and fingerprint analysis
• Innovative 2D gel analysis with powerful databasing and querying
• Comprehensive sequence and chromosome analysis
• Exploration of high-throughput microarray and genechip expression data
• Combined querying, mining and analysis of all aforementioned data types
• Numerous supervised and unsupervised learning techniques and statistical tests

A large number of free Plugins available for specialist applications, automation, advanced analysis tools, reporting, etc.

Software Link : BioNumerics - Bioinformatics software 

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