Hui Li et al. recently investigated the transcriptional activity of C/EBP-â, and have published their findings in the Journal of Biological Chemistry, after identifying unique folds using RAPTOR for protein structure prediction. As the authors state, “transcription factor C/EBP-â is crucial for regulating transcription of genes involved in a number of diverse cellular processes, including those involved in some cytokine-induced responses. However, the mechanisms that contribute to its diverse transcriptional activity are not yet fully understood.” The use of transcriptional mediator regulates signal-induced cellular gene transcription from enhancer-bound transcription factors in the multi-subunit protein complex. As is the rising case with many researchers, the preferred method for determining the protein structure was completed successfully using RAPTOR. The preference comes from its strength in hard targets, cases with low or no sequence homology. Typically, given a target protein sequence, comparison with a homologous protein with known structure 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 sequence homology is not significant, i.e. less than 25%, PSI-BLAST and BLASTP can not provide confident result. 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 no sequence homology. In this particular case domain confirmation was modeled in addition to accurately identifying the critical region of cellular factor of C/EBP. BSI would like to congratulate each researcher of this project on their investigation and findings. Contributing authors include: Hui Li, Padmaja Gade, Shreeram C. Nallar, Abhijit Raha, Sanjit K. Roy, Sreenivasu Karra, Janardan K. Reddy, Sekhar P. Reddy and Dhananjaya V. Kalvakolanu.

Bioinformatics Solutions Inc (BSI) would like to applaud two "best paper awards" by BSI authors Ming Li and M. Ziaur Rahman, in prestigious international conferences this year (2007). “FragQA: predicting local fragment quality of a sequence-structure alignment,” by Li and his students at University of Waterloo, claim the Best Paper Award at the Genome Informatics Workshop (GIW) in Singapore. The report is expected to add an important component to RAPTOR, for predicting protein structures. GIW is the longest running international bioinformatics conference, devoted to the computational understanding of biological systems on a molecular basis. M. Ziaur Rahman and University of Waterloo SCS Professor J. Ian Munro won the “Best Paper Award” for their report “Integer Representation and Counting in the Bit Probe Model” presented at the 18th International Symposium on Algorithms and Computation (ISAAC) 2007 in Sendai, Japan. The research paper addresses the methodology of representing integers so that updates to values can be performed in a power efficient manner. ISAAC is currently hailed as the leading field of Algorithms conference in the Asia-Pacific region. Rahman has recently accepted a position at BSI as a software developer and research analyst for RAPTOR.

Bioinformatics Solutions Inc, (BSI) producer of the highly accredited, globally popular PEAKS peptide mass spectrometry software, announced today its latest server/cluster solution, PEAKS Online 2.0. PEAKS gives greater coverage and confidence -- a more complete understanding of protein samples -- in one shot, using renowned de novo sequencing and protein identification algorithms. Ideal as a shared resource, this latest release of PEAKS Online, the high throughput webserver/cluster, now includes industry grade security and user management. System administrators can empower users and research groups to share resources without compromising security. PEAKS Online provides a forum for efficient collaboration. Free trial users can process multiple tests at once by harnessing the powerful PEAKS public server. Load in a private or public database and see the results on your own data using built-in and customizable enzymes and modifications. Be among the first to investigate this new tool at no charge. Sign up for PEAKS Online at www.bioinfor.com/peaksonline. To read RAW data, inChorus (automatically compare results with Mascot, Sequest, X!Tandem, etc), manual de novo sequences or find homologous peptides using SPIDER, connect PEAKS Client to PEAKS Online.

Waterloo software developers, BSI (Bioinformatics Solutions Inc.) announced, today, their much anticipated release of PEAKS 4.5 for peptide mass spectrometry analysis. PEAKS, known for its leadership role in de novo sequencing (sequencing of peptides not present in any database) is once again guiding tandem mass spectrometry researchers into in a new era of data analysis through sequence reconstruction. Accurate sequence reconstruction is performed by the built in SPIDER tool, which has been demonstrated to increase peptide findings by upwards of approximately 20%. Other cutting-edge enhancements to PEAKS help researchers to identify peptides using predicted retention time. PEAKS provides all of the necessary tools for superior peptide sequence derivation and protein identification from tandem MS/MS spectra - all within an intuitive graphical interface. PEAKS Studio 4.5 provides fast, accurate results for spectra from both sequenced and unsequenced organisms. Instrument Capabilities: Researchers are now fully capable of processing raw data, straight from their instruments (Agilent, Bruker, Shimadzu, Thermo and Waters to name a few). Visit www.bioinfor.com for more details.

BSI is proud to announce the release of RAPTOR 4.1 for Linux and Windows, the latest edition of protein threading software. RAPTOR is an innovative software tool designed to predict protein structure from protein sequence. Armed with unique integer programming algorithm, RAPTOR is capable of discovering remote structural homology for hard sequences and giving high quality prediction. As a participant in recent CASP's, RAPTOR has been consistently ranked in the top tier. In addition to the three threading methods proprietary to RAPTOR, the new version integrates PSI-BLAST for rapid identification of easy targets. A built in pipeline in RAPTOR 4.1 allows users to automatically run more rigorous threading techniques if necessary. RAPTOR 4.1 is your protein structure pipeline, right out of the box.

Today, Waterloo software developers, Bioinformatics Solutions Inc. have launched their latest suite of proteomic software, PEAKS Studio 4.2. Among the preliminary benefits, de novo sequencing and protein identification, the latest advancements include faster processing time, simple reporting and improved exporting features. These are all provided in an attempt to reduce research time and increase accuracy. The software was released to the public following email notification of the upgrade to current customers. “Speed and efficiency were our goals for the new release,” says Iain Rogers. “Our focus has resulted in users being able to not only view their results quickly, but in the format and order they prefer.” An example is users can now view only publishable results: proteins identified by more than one high scoring peptides. Result reports can be filtered by a number of criteria (delta mass, proteins with X# of good hits inclusive and exclusive, etc). A simple report to summarize de novo sequencing on a whole run has been included. Further, the scans may now be sorted by scan number, mass, m/z, or retention time. The de novo options screen allows users to limit the number of variable modifications allowed in a proposed de novo sequence. In regards to exporting data to other locations PEAKS 4.2 allows use of spectra images, spectra with ions annotated, sequence-spectrum alignment, ion tables and error plots can now be exported in high resolution for printing. WYSIWYG (What You See Is What You Get) export of protein ID results, both from ‘peptide view’ and ‘protein view’ has been enabled. The embedded software, SPIDER, Software Protein Identifier, has been recalibrated for increased speed (several fold), along with accuracy. Perhaps the largest problem of the field of research is the multiple variations of file formats produced. In an attempt to create a uniform format, PEAKS supports HUPO’s (Human Proteome Organization) proposed file format standard: mzData. Preliminary testers are raving about the new appearance of PEAKS and that is generally a good sign of the success in Mr. Rogers’ focus into user coherence.

Bioinformatics Solutions Inc. is proud to announce the release of RAPTOR 4.0 for Linux, the latest edition of protein threading software. RAPTOR is an innovative software tool designed to predict protein structure from protein sequence. Armed with unique integer programming algorithm, RAPTOR is capable of discovering remote structural homology for hard sequences and giving high quality prediction. As a participant in recent CASP's, RAPTOR has been consistently ranked in the top tier. RAPTOR 4.0 has a completely revamped GUI, which is considerably more interactive and easier for users to run sequences. The outputs are visualized vividly with consistent color scheme and users can easily understand the outputs. Users can try three different threading methods one by one in the GUI. The well designed configuration panel makes it possible for new users to set up RAPTOR in a few seconds. RAPTOR 4.0 has well designed interface and works seamlessly with Modeller. In addition, RAPTOR 4.0 can also generate ICM Pro input files. RAPTOR 4.0: Same effort, Even better output.

A growing Canadian company, Bioinformatics Solutions Inc, specializing in mass spectrometry software, just confirmed a partnership with the world's largest Mass Spectrometer (instrument) manufacturers, Thermo Electron Inc., in West Palm Beach Florida, Tuesday.

VP of Business Development, Iain Rogers, was excited after presenting the recently released PEAKS Studio 4.0 software to Thermo's head Training and Support Representatives. PEAKS Studio 4.0 uses de novo (from scratch) sequencing and protein database search techniques to identify known and unknown peptides, for drug discovery.

“The presentation was only an hour long so my words had to resonate with their corporate identity. Thermo strives to make their mass spec solution the most capable, and is looking to specialists like BSI to complete the picture. Constructive discussion centered on how to integrate PEAKS de novo sequencing and sequence tag based protein characterization tools with Thermo's BioWorks package.”

The recent good news for the Waterloo, Ontario based company is “a pleasant addition to the bustling new office," addressed Managing Director, Luosha Lu. "The recent release of PEAKS Online and PEAKS Q has been well received as have our latest versions of Raptor, PatternHunter and ProsepectPro. Bioinformatics Solutions is not shy to requests such as the Thermo partnership," Rogers reports, “BSI customized its software to such major brands as Thermo Electron, long before this opportunity came into scope.”

Bioinformatics Solutions Inc. have just released PEAKS Q, a Software for MS-based Quantification of Stable Isotope Labeled Peptides.

Several mass spectrometry-based stable isotope labeling technologies have been developed for global proteome profiling. These include methods for in vivo labeling, such as 14N/15N and SILAC (Stable Isotope Labeling with Amino Acids in Cell Culture), and in vitro isotope labeling of target peptides at their N/C terminal or at specific residues. PEAKS-Q, was designed to automatically identify and quantify proteins from these isotope labeling experiments. The software is written in Java and includes an intuitive graphical user interface.

In preliminary testing, PEAKS Q has demonstrated to be robust and an easy to use software for quantification of peptides from mass spectrometry. Its protein quantification accuracy is well within experimental error, and significance of abundance changes between samples is easy to see. Inquires for a copy of the free beta version can be located on the PEAKS Software Download page.

Bioinformatics Solutions Inc. (BSI) is proud to announce the release of the much anticipated PEAKS Studio 4.0. The latest in de novo sequencing and protein identification software yielding accurate results fast. By automatically filtering out insufficient quality results before database searching users can get the most out of low resolution data. Further, an increase in coverage is obtained by using four search engines for protein identification, instead of just one.

A new Software Protein IDentifiER, SPIDER, has also been bundled with PEAKS Studio 4.0. This sequence tag based search tool confidently identifies peptides using the de novo sequences derived by PEAKS auto de novo sequencing. Users can find protein information even in unstudied organisms, or find sequence variation between samples. SPIDER differs from regular homology search tools in that it was designed to account for inherent de novo sequencing errors like: (I/L), (N/GG), (SAT/TAS). More details regarding new features can be obtained here.

Bioinformatics Solutions Inc. moved its headquarters to a new location to accommodate the addition of several new team members. The long awaited move sees BSI in a bright and spacious office at 204-470 Weber St. North, in Waterloo, Ontario, (N2L 6J2). Email, web servers and phone systems were all transferred smoothly, so interested parties may still reach us at through the usual channels. Contact us.

You can now try the renowned PEAKS de novo sequencing and protein ID software using your web browser. Bioinformatics Solutions Inc. has opened access to the PEAKS Online server cluster. With a few mouse clicks, researchers worldwide can use their web browsers to submit MS/MS data and view results in moments. PEAKS Online is the web version of PEAKS Studio that has been designed with high throughput data analysis in mind. MS/MS data analysis has never been this fast, accurate, and simple!

PEAKS Online is available to the public at:
http://www.bioinformaticssolutions.com/peaksonline/.
Non-registered users are only limited by the amount of data they can submit daily.

Waterloo software developers, BSI (Bioinformatics Solutions Inc.) announced their latest release of PEAKS Online. PEAKS Online is a auto de novo and protein identification software that works on a computer cluster for enhanced performance. On a cluster, PEAKS Online shares the processing of MS/MS data between multiple computers. This decreases the data analysis to a fraction of the stand-alone type computational time.

There is a big difference between the initial version and this one. The overall computation is at least 4 times faster due to changes in to both the auto de novo and protein ID algorithm’s efficiency. A taxonomy feature borrowed from PEAKS Studio has been implemented in this new version. A new user defined PTM (Post-translational modification) customization tool has also been added to the data submission window. Other small changes to the GUI have been made based on our customer input.

We are convinced that our users will be impressed with the improvements found in PEAKS Online 1.1.

Waterloo software developers, BSI (Bioinformatics Solutions Inc.) announced their latest de novo sequencing and protein identification software, PEAKS 3.1 today.

This is the fastest PEAKS to date. PEAKS Studio 3.1 boasts an increase in speed as high as 400% with some MS/MS data. The algorithms for both protein identification and de novo sequencing have been improved. There is also an improvement in the overall accuracy of the results.

To indirectly improve the overall speed and accuracy of PEAKS Studio, the development team has included a taxonomy search feature. The taxonomy add-on allows our users to specify the taxonomy of the organism under study. This focuses the protein ID search to a small subset of proteins, which shortens the search time.

PEAKS has matured a great deal in the 4 years since its first release and version 3.1 adds a great deal to the overall performance and stability of the product.

Bioinformatics Solutions Inc. (BSI), an advanced bioinformatics software provider announced its opening of its new branch, Beijing Bioinformatics Solutions Inc. (Beijing BSI), in Beijing China. The new branch started operation in August 2005, and is physically located in Tsinghua University high-tech incubator.

BSI was founded in 2000 as a spin-off from the University of Waterloo. The headquarters of the company are near the University in Waterloo, Ontario, Canada. The company's renowned bioinformatics products include PEAKS for protein identification from mass spectrometry, PatternHunter for homology search, and Prospect/Raptor for protein structure prediction. Over one hundred reputable customers worldwide have subscribed BSI's products. The opening of its Beijing branch is regarded as a step further to become an international bioinformatics solution provider.

Welcome to the new face of BSI. The site is now organized according to the solutions we offer (see left). We hope the new arrangement will help you find the information you were looking for much quicker.

But it's not just about our products; it's also about you, our users, and the community at large. We hope to provide a space for you to share your research and your oppinions about our software. In this way we can learn from eachother.

Waterloo software developers, BSI (Bioinformatics Solutions Inc.) announced their latest de novo sequencing and protein identification software, PEAKS 3.0 today.

PEAKS 3.0 boasts an advance in protein identification technique. BSI has developed a meta search protein identification tool called "inChorus protien ID". This allows researchers to cross check their findings automatically. PEAKS 3.0 launches other search tools and integrate the results from all searches. Iain Rogers, part of the research team at BSI expressed this feature as “Get the right answer in one shot.”

PEAKS 3.0 also uses tandem mass spectrometry data to find peptide sequences with our without the aid of a database. PEAKS technology prides itself as being the fastest, most accurate auto de novo sequencing algorithm on the market. It provides a complete sequence for each peptide, confidence score on individual amino acid assignments, simple reporting for high-throughput analysis, and all the information a researcher needs for in depth investigation. PEAKS provides all of the tools necessary for superior peptide sequence derivation and protein identification from tandem MS spectra - all within an intuitive graphical interface. Complete with auto de novo sequencing, manual de novo sequencing and protein database searching technology, PEAKS Studio 3.0 provides fast, accurate results for spectra from both sequenced and unsequenced organisms.