Cryptography with DNA binary strands

Biotechnological methods can be used for cryptography. Here two different cryptographic approaches based on DNA binary strands are shown. The rst approach shows how DNA binary strands can be used for steganography to provide rapid encryption and decryption. It is shown that DNA steganogra- phy based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages. The second approach shown here is based on steganography and a method of graphical subtraction of binary gel-images. It can be used to constitute a molecular checksum and can be combined with the rst approach to support encryption.

full article at http://www.cs.mun.ca/~banzhaf/papers/DNA_Crypt_final.pdf

Bioinformatics Techniques for spam detection

Its not a new topic IBM has discovered that it could use many of the pattern detection techniques and analysis used in bioinformatics in other fields as well.

I thought of adding this as bioinformatics is and microarrays are growing in popularity and decided to give few bytes such articles as wel.

Many of these studies are based on the homology detection. Perhaps going forward the techniques used in SNP detection in SNP microarrays might also find use in other fields notably in spam detection and share market analysis or trends analysis

I find some of the presentation onthe web andd from IBm on using the famous Teiresias algorithm, for spam detection

Chung-Kwei applies advanced pattern matching algorithms developed in IBM’s bioinformatics group to spam detection. This new classification algorithm can detect complex patterns in messages that go beyond the simple word or word phrases used in most algorithms.

A technique originally designed to analyse DNA sequences is the latest weapon in the war against spam. An algorithm named Chung-Kwei (after a feng-shui talisman that protects the home against evil spirits) can catch nearly 97 per cent of spam.

Chung-Kwei is based on the Teiresias algorithm, developed by the bioinformatics research group at IBM’s Thomas J Watson Research Center in New York, US. Teiresias was designed to search different DNA and amino acid sequences for recurring patterns, which often indicate genetic structures
that have an important role.

Instead of chains of characters representing DNA sequences, the research group fed the algorithm 65,000 examples of known spam. Each email was treated as a long, DNA-like chain of characters. Teiresias identified six million recurring patterns in this collection, such as “Viagra”.

Each pattern represented a common sequence of letters and numbers that had appeared in more than one unsolicited message. The researchers then ran a collection of known non-spam (dubbed “ham”) through the same process, and removed the patterns that occurred in both groups.

Genuine email Incoming email was given a score based on how many spam patterns it had. A long email that only had a few spammy sentences would get a relatively low score; but one with many patterns spread across the length of the message would score much higher. The Chung-Kwei correctly identified 64,665 of 66,697 test messages as being spam or 96.56 per cent. More importantly, its rate of misidentifying genuine email as spam was just 1 in 6000 messages. Losing a single email in a torrent of spam is a greater failing in a filter than letting the occasional spam email through.

Chung-Kwei deals with common spammer strategies to dodge pattern-recognition schemes, such as replacing the s with a $, as in “increa$e your $ex power” using its built-in tolerance for different, but
functionally equivalent, DNA sequences. Just as in genetic analysis, Teiresias could be taught that CCC and CCU codons both produce the same amino acid, proline, the anti-spam system an be trained to accept $ and s as identical.

IBM intends to include Chung-Kwei in its commercial product, SpamGuru. Justin Mason, who developed SpamAssassin, one of the most popular open-source anti-spam filters, says that Chung-Kwei looks promising.

 

 

 

DNA Analysis Could Boost Accuracy Of Thyroid Tests

Source: http://www.medicalnewstoday.com/sections/genetics/

By fine-tuning “fine-needle aspiration” biopsies with a super-fast genetic microarray technology, a team of surgeons from NewYork-Presbyterian Hospital/Weill Cornell Medical Center in New York City says they can greatly enhance the accuracy of these tests.

“For patients with worrisome thyroid nodules, this means better information on whether the nodule is malignant or benign. That should help them and their doctors make better decisions as to what treatment they’d like to pursue,” explains senior researcher Dr. Thomas J. Fahey III, associate professor of surgery and Frank Glenn Faculty Scholar in Surgery at Weill Cornell Medical College, and associate attending surgeon at NewYork-Presbyterian Hospital/Weill Cornell Medial Center in New York City.

In the study, the team created microarray-generated “gene expression profiles” from fine-needle aspirates by comparing the expression of thousands of genes from both cancerous and benign thyroid tissues. This process ended in a grouping of 25 differently expressed genes that helped distinguish malignant from benign growths.

“We next tested the accuracy of these patterns using 22 fine-needle aspirate samples from benign or malignant thyroid nodules,” Dr. Lubitz explained.

“In all but one case, the microarray test agreed completely with the results of extensive histological analysis in the lab,” she said.

According to the researchers, a move from histological to microarray analysis of thyroid aspirates could impact anywhere from 5 to 25 percent of patients undergoing this kind of diagnosis — giving them a better grasp of whether they might require surgery, for example.

Cost remains a factor, with a single microarray screen currently totaling about $500. “We anticipate, however, that as this technology becomes more widespread and improves, the price per test will fall much lower,” Dr. Fahey says.

DNA microarray–based analysis may be useful for assessing the risks and benefits of hormone therapy

Hormone-replacement therapy influences gene expression profiles and is associated with breast-cancer prognosis. The US FDa has apprved use of two new microarrays for clinical decision making. The US Food and Drug Administration (FDA) encourages the development of new technologies such as microarrays which may improve and streamline assessments of safety and the effectiveness of medical products for the benefit of public health. The FDA anticipates that these new technologies may offer the potential for more effective approaches to medical treatment and disease prevention and management. One of the new application for microarrays apart from use in cancer treatment could be in Hormone replacement therapy. A study has been publoished using microarrays to identify modifications in the gene expression profile of the ocular posterior segment in ovariectomized (OVX) mice with and without substitutive estradiol therapy. some of the other studies can be viewd at

http://www.biomedcentral.com/1741-7015/4/16

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1555602

Microarrays and Toxicogenomics service for Drug development

Microarrays are finding more usage in drug discoverry and development process, toxicogenomics and pharmacogenomics studies have helped researchers to speed up the druug discovery to process, though it is still long way to produce any immediate effect to the patients. The use of toxicogenomics and comparative genomics studies can help scientists to unearth new therapeutic uses for existing drugs. Ocimu biosolutions alon with its services in preclinical and toxicogenomics studies is looking forward to acheive this by helping pharmaceutical companies to conduct toxicogenomics services, by tapping into its cost effective India research centrre while maintiaing a high degree of expertise by using a clutch of researchers from US and europe alike.

microarray for transgenomics studies and Study of Evolution of organisms

Barcode microarrayshas demosntrated the various ways in which the microarrays can be used in various ways.Though mirred in controvesy as any new technology has been subjected in its infancy, the basic principles behind the technology can be put to use in many other frontiers. It may be optimized to study transgenomics organims and its evolution. To study the development of drug resistance bacteria and virus. To find out how microbes evolve though all this may require new approaches it all could stem from the basic principles adopted by DNA microarry and barcode microarray and SNP arrays

Microarrays for taxonomics studies

The develpment of barcode microarray may be a subject of debate , but it may hel in transgenomic studies, and would help in finding new avenues for use of microarrays

microarray data as Phenotype

Microarrays provide a method of quantifying the expression and order of genes in a particular genome — acting as a surrogate measure of cell physiology, said researchers at Baylor College of Medicine in a report that appears online today in the journal Nature Genetics.

“Microarray data are good phenotypes to determine the order of genes and are a good surrogate measure of cell status,” said Dr. Gad Shaulsky, associate professor of molecular and human genetics at BCM.

Microarrays are fairly new technology that can help scientists understand how genes interact as well as how they are regulated by networks within the cell. They are created by the placement of tiny droplets of functional DNA on glass slides. Then researchers attach fluorescent labels to nucleic acids (DNA or RNA) from the cells under study. These labeled nucleic acids are allowed to bind to the DNA on the slides. Researchers then use a microscope to measure how much of a specific nucleic acid is present.

Genotype is the genetic fingerprint of a particular cell. Phenotype is the outward manifestation of the genotype. For example, a person may have genes for eye color. That is that individual’s genotype. Blue eyes is the phenotype.

The microarray data Shaulsky and his collaborators used show that they can determine the order in which genes act in a cascade that results in a particular phenotype.

Shaulsky and his co-authors performed their work in Dictyostelium (Dictyostelium discoideum), a form of soil amoeba used in the laboratory because many of its 10,000 genes are homologues or equivalents of genes found in humans.

Using microarray data alone, they determined the orders in which genes function in a particular pathway in that organism. The protein kinase A (PKA) signaling pathway occurs when the organism encounters starvation. The pathway enables the single cells to combine into a multi-cell organism.

“We pretended we did not know the order of genes in the pathway,” said Shaulsky. “We were able to reconstruct the pathway from the microarray data. This means the microarray provides a good phenotype that is quantitative. We can prove that gene A comes before gene B and give mathematical support for these findings.”

“This is a proof of principle that we set out to do – assessing the function of unknown genes is feasible,” said Shaulsky. “It can be done with a microarray phenotype.”

Others who participated in the research included Drs. Nancy Van Driessche, Ezgi O. Booth, Paul Hill and Adam Kuspa, all of Baylor College of Medicine; and Janez Demsar, Peter Juvan and Blaz Zupan of the Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.

Source : Baylor College of Medicine

Consolidation in Oligo industry and Growth for India based companies and outsourcing value proposition in Genomics and microarray/oligo industry

Ocimum Biosolutions acquires European based Oligo manufacturing company – Isogen Life Science

November 17, 2006, IJsselstein/Hyderabad – Ocimum Biosolutions, a leading provider of laboratory information management systems (LIMS), bioinformatics solutions, Microarrays and contract research headquartered in Hyderabad, India, has acquired the BioMolecules synthesis business of Isogen Life Science based in The Netherlands. Ms. Anuradha Acharya, CEO of Ocimum Biosolutions said “We are very pleased to have taken a significant step towards becoming a global oligo player with the Isogen acquisition. We will continue looking for targets in related areas to scale up our oligo production capability. This acquisition will also help us become a more integrated genomics services provider with three delivery points in Indianapolis, IJsselstein and Hyderabad.” Mr. Hans Beijersbergen van Henegouwen, MD of Isogen Life Science said, “It is an excellent opportunity for the Biomolecules Division of Isogen Life Science to become a global player in this competitive business. The new business configuration will be much more flexible and will be able to play an important role in the vast growing demand for oligo nucleotides all over the world. Ocimum is the perfect partner for fulfilling a broad platform of needs in this market segment.” Avendus Advisors was the sole financial advisor to Ocimum for the deal. Commenting on the transaction, Shiraz Bugwadia, A.V.P., Avendus Advisors “Ocimum is one of the few Indian players within the BioIT and microarrays space to have scaled up successfully over the last couple of years. Ocimum has also been successful at using the inorganic route to scale rapidly by acquiring niche good quality companies in Europe such as MWG Biotech’s division and now Isogen Life Science.” About Isogen Life Science: Isogen Life Science (www.isogen-lifescience.com) is a leading supplier of products for the life science sector. The company provides a wide range of instruments, reagents and consumables in the areas of cell biology, molecular biology and biochemistry. Isogen Life Science is a merger between B&L Systems (1987), the Benelux distributor for scientific instrument companies, and Isogen Bioscience (1988), a leading producer of DNA, RNA, peptides and related products, which are used around the world by pharmaceutical and biotechnology companies and leading research institutes. About Ocimum Biosolutions: Ocimum Biosolutions is a life sciences R&D enabling company with three main focus areas, BioIT, Microarrays and Contract research services. The US operations of the Company focuses on custom contract research services in the molecular biology area while the Indian operations provide BioIT services and Microarrays. Ocimum has more than 300 prestigious clients worldwide including the Centres for Disease Control, University of Toronto HIV clinic, National Research Council of Canada, Dow AgroSciences, Max Planck Institute etc. Ocimum has adopted an inorganic strategy to ramp up the business fast and has demonstrated its capability to execute this strategy in the past. As a part of its strategy, Ocimum acquired a division of MWG Biotech, Germany in 2005. The Company has received a host of awards and recognitions. The Company has recently received the IT Innovation award by NASSCOM, presented by H.E. the President of India. Also, Red Herring magazine picked Ocimum as one of the eight compani es to watch in India. Deloitte ranked the Company as 4th Fastest growing Technology company in India and the Fastest growing Life Sciences Company in India. For more information, please visit: www.ocimumbio.com

Indian company gets 6.5 million USD IFC funding to promote contract research in bioinformatics and genetics industry

Hyderabad, November 15, 2006 – Ocimum Biosolutions today announced that International Finance Corporation (IFC), the private sector arm of the World Bank Group, will invest USD 6.5 million of equity, for a minority stake, and debt in the Company. Funds raised from this transaction will be used for financing both organic as well as inorganic growth of the Company.

Says Ms. Anuradha Acharya, Founder & CEO of Ocimum Biosolutions, “We are very happy to have IFC as our partner for growth. These are exciting times for Ocimum and to have IFC as an investor in the company brings a lot of confidence in our clients and partners.”

Iyad Malas, IFC’s Director for South Asia, said, “IFC’s support to Ocimum will provide the company its much needed growth capital to establish an internationally competitive contract research outsourcing company and promote the discovery of new drugs at lower costs. We will also help institute improved corporate governance standards.”

This is Ocimum’s first round of fund raising from private equity investors. The Company is contemplating another round of fund raising in the next 18-24 months.

Recently, Ocimum acquired a Europe based oligo manufacturer. The Company is also scouting for more targets in the European market.

Avendus Advisors was the sole financial advisor to Ocimum for the deal. Commenting on the transaction, Shiraz Bugwadia, A.V.P., Avendus Advisors “Ocimum is one of the few Indian players within the BioIT and micro arrays space to have scaled up successfully over the last couple of years. Ocimum has also been successful at using the inorganic route to scale rapidly by acquiring niche good quality companies in Europe such as MWG Biotech’s division and now a Netherlands based oligos manufacturer.”

About Ocimum Biosolutions:

Ocimum Biosolutions is a life sciences R&D enabling company with three main focus areas, BioIT, Microarrays and Contract research services. The US operations of the Company focuses on custom contract research services in the molecular biology area while the Indian operations provide BioIT services and leverage on India’s low cost advantage in IT space. The Company enjoys a strong brand image in the market and has worked with some of the best research organizations in the world like IIT Kharagpur, National Research Council of Canada, Agriculture and Agri Foods, NIH, Dow Agro Sciences, etc.

Ocimum has adopted an inorganic strategy to ramp up the business fast and has demonstrated its capability to execute this strategy in the past. As a part of its strategy, Ocimum acquired a division of MWG Biotech, Germany in 2005. The Company has received a host of awards and recognitions. The Company has recently received the IT Innovation award by NASSCOM, presented by H.E. the President of India. Also, Red Herring magazine picked Ocimum as one of the eight companies to watch in India and was a winner of Red Herring’s Asia 100. Deloitte ranked the Company as Fastest growing life sciences company in India.

For more information, please visit: www.ocimumbio.com.

About International Finance Corporation:

The International Finance Corporation, the private sector arm of the World Bank Group, is the largest multilateral provider of financing for private enterprise in developing countries. IFC finances private sector investments, mobilizes capital in international financial markets, facilitates trade, helps clients improve social and environmental sustainability, and provides technical assistance and advice to businesses and governments. From its founding in 1956 through FY06, IFC has committed more than $56 billion of its own funds for private sector investments in the developing world and mobilized an additional $25 billion in syndications for 3,531 companies in 140 developing countries. With the support of funding from donors, it has also provided more than $1 billion in technical assistance and advisory services.

For more information, please visit www.ifc.org.

standardization in microarray analysis software industry

scouting for the right software for the microarray analysis software , kept me thinkng why despite these software being used by scores or scientists no one has come forward to create what can be called as a standard for such software, the confusion rains in this field as one company’s software data do not work with another one and vice versa, For an industry like biology and drug discovery  that is trying to benefit from the knowledge of mathematics statitics and chemistry physics inability to port data across platform is a serious roadblock. there are standards such as MIAMe and MAGE but these are just data standards, not for softwares, I believe ther should be  something similar to ISO standards, SEI CMI etc.

majority of the newsgroup and forums are used by graduate and at times senor researchers to find out which is the best software to be used, I thought of starting a wiki page where researchers can post their comments and rate the products and compare the features against each other,

can open source ideals begin to give a real answer to biotech’s future

would it be possible to adopt the ideals of the open source in microarray development, there has been many research works that can be hailed as open source ideals in the biotechnology space, human genome project can be the perfect example, But apart from the few attempts by academia and non profits institutions there havnt been many attempts to look at this as a way forward, Microarray development can be termed as a lucrative field where such a coalition would accrue great benefits, By releasing the research works for others for free of cost it is possible to bring down the cost of microarray, there is no doubt that it would benefit the new research frontiers such as pharmacogenomics and toxicogenomics, by reducing the cost per array closer to any to other screening test currently adopted in hospitals or used by forensic labs. Microarray can also be used for reducing the costly PCR technique by closing in on a more focused number of genes to amplify from But it would mean that there has to be enough researchers out there who will be buying theses product in the first stage itself so as the company involved i such an audacious attempt would recover its cost and make profits to continue further work, thats a major hurdle to overcome, as custom microarray or at times even the existing one may not be useful to every researcher even if they are working on the same genome for example one person may be in toxicology research and the other in ecology or pure genetics even if they work on same genome the controls required and number of gene of interest would vary vastly across the spectrum, it may take a long time for the open source ideals to bear any fruit in this arena but that may be the way forward to bring meaningful results with less cost, till outsourcing can be a start for all things to come

 Abin paul Xavier

http://www.ocimumbio.com

benefit by outsourcing your custom array projects

new companies in India can do the otherwise costly custom microarray projects with much reduced price and as one of the most expensive part of the custom projects are the design of the custom oligo and its synthesis companies who can outsource these works to india;s postdocs and postgraduates in statics and informatic and biotech can save a lot these cost for the researchers, A new host of companies such as ocimum biosolutions  are doing just this. For example the Institute of Bioinformatics a non-profit organisation set up by the ‘The Genomics Research Trust’ in collaboration with the University of Hopkins at the International Tech Park, Whitefield, Bangalore. Other companies like Ocimum Biosolutions has worked with instituoins like NIH and CDC and has also proved itself by taking over companies like MWG biotech’s microarray division and Isogen life science for modified Oligo and now offers microarrays oligo and research services apart form LIMS

microarray software

Ocimum Biosolutions is a life sciences R&D enabling company with three focus areas, BioIT, Microarrays and Research services. The Microarray division of Ocimum has been recently acquired from MWG Biotech. These include Catalog “OciChip”, Custom “OciChip” and microarray services.

Ocimum biosolutions offers an                       microarray analysis software called Genowiz, An evaluation copy of the software is avaialble at http://www.coimumbio.com

Genowiz™ Genowiz™ is a powerful gene expression analysis program that has been designed to store, process and visualize gene expression data efficiently. It includes a suite of advanced analysis methods and allows researchers to select analysis methods appropriate for their dataset. Genowiz™ allows researchers to organize experimental information (MIAME), import data files quickly and easily, work with multiple experiments at the same time, import gene annotation files, pre-process and normalize data, perform cluster analysis, classify and view gene information, perform functional classification and track down intricate correlations in data by performing pathway analysis. All analysis done is tracked, saved into a database and can be retrieved at any point of time.   What’s New • Import Affymetrix Raw Data • Merge Clusters • One Sample t-Test • SVM • View and Update NetAffx™ Annotations • Annotation Views • URL Editor • Search for Gene Ontology and Pathway terms • Regulatory, Signal Transduction and Disease Pathways Data and Gene List Import Genowiz™ supports a wide range of data formats pertaining to cDNA and Affymetrix data. Users can directly import .CEL and .CDF files into Genowiz™. Users also have an option to upload data in customized formats. Customized uploader allows users to add and save new data formats. One-Click Uploader can then identify these formats. Gene List files for annotating genes can also be imported. MIAME Minimum Information About a Microarray Experiment (MIAME) facilitates adoption of standards for microarray experiment annotation and data representation. Genowiz™ focuses on establishing standard microarray experimental data repositories and information sharing within the scientific community. Researchers can also exchange MIAME data by using MAGE ML document exchange format. Data Transformation, Normalization and Filtration In any type of expression analysis, pre-processing of data to reduce undesirable variation among datasets and to bring data to a common platform is a vital step. Genowiz™ provides users with a wide range of data transformation, normalization and filtration tools. These include: • Data transformation options such as imputation of missing values, log transformations, mean/median, Z-transformation, subtract control, divide by control, scaling etc. • Normalization techniques such as normalization for dye swap replicates, cDNA raw data normalization options (cDNA Loess and Print tip Loess) and quantile normalization. Separate normalization techniques are provided for cDNA and Affymetrix arrays. Normalization can be done using all genes or control genes. • Filter data based on replicate genes, fold change, mean, standard deviation, calls and missing values. Replicate samples are handled using various parametric/non-parametric tests. Multiple testing correction can be applied to reduce false positives. Data Analysis and Visualization Genowiz™ comes equipped with several data analysis tools. Complete with excellent graphics, it is an excellent tool for interpretation of biologically meaningful results. Some of these tools include partition clustering, hierarchical clustering, SOM, PCA, gene shaving and discriminant PCA and SVM. Option for merging, clusters of interest has also been provided. • Partition Clustering (K-means, Forgy’s) This tool classifies genes or samples in user-defined groups using distance parameters. The obtained clusters can be re-clustered. Re-clustering utility helps scientists pick a set of genes of their interest. A 2D PCA view shows the distribution of genes in various clusters. • Hierarchical Clustering One of the most important tools for studying relations between genes, this tool creates a dendrogram based on the relative distance between genes. The different optional parameters help the user in correctly determining the relationship between two genes. Models of analysis include single linkage, complete linkage and average linkage clustering. Genes, samples, or both together can be clustered. • Self Organizing Maps A two-way classification of genes into clusters based on novel artificial neural networks is an integral feature of data clustering tools in Genowiz™. This gives a deeper insight into clusters, as neighboring clusters are very similar to each other. • Principal Component Analysis This tool involves a mathematical procedure that transforms a number of (possibly) correlated variables into a (smaller) number of uncorrelated variables called principal components. These provide an insight into existent variability in the data. • Gene Shaving This method identifies subsets of genes with coherent expression patterns and large variation across conditions. Gene shaving differs from hierarchical clustering and other methods of gene expression analysis in that genes may belong to more than one cluster. Classification Classification algorithms are used to classify samples, based on information from similar samples with known classes that are available in training data. In Genowiz™, Support Vector Machines (SVM) and Discriminant PCA are used to predict classes for unclassified samples. Biological Analysis Genowiz™ annotates genes and classifies them into functional categories (Gene Ontology). Option of importing annotation files is also provided. Integrated pathways module aids researchers in understanding metabolic pathways in relation to expression data. Pathway maps edited/created can be associated with author details too. Coupled with biological information and gene ontological classification, it forms an excellent tool in understanding biological systems. Search can be performed on the gene ontology and pathway tree to look for ontologies or pathways of interest. Utilities Several utility options are present to add value to the analysis performed: • Gene List Comparison: Subtle relations among datasets can be probed using this feature. • Pattern Simulation: An expression pattern can be defined and Genowiz™ lists out all genes with a similar expression pattern. This gene list can be saved and exported. • Gene Tracking: Important genes or genes of interest can be tagged and tracked throughout the analysis. View and Update NetAffx™ annotations Annotations for the uploaded data can be viewed by connecting to NetAffx™ database. Connecting to the NetAffx™ database and selecting a corresponding chip will retrieve annotations from that chip. Flexibility to update annotation information for existing chips and add annotation information for new chips is also present, thus enabling researchers to view updated annotations for chips. Technical Support Ocimum’s technical support staff is available 24 hours, five days a week, to answer your questions about Genowiz™ over phone, e-mail and web chat. All questions previously answered by the support staff are available on the website for visitors. Sytem Requirements:   Request FREE trial

microarray from ocimum biosolutions

Ocimum biosolutions offers microarays and bioinformatis sofftware to researchers across the world, The microaray division of ocimum offers the MWG chips which were earl;ier manufactured by MWG biotech of Germany

for more detail visit http://www.ocimumbio.com

OciChip™ Design – Route to a perfect Array

OciChip™ design and production concept ensure the highest microarray quality.

First, sophisticated bioinformatics design chips of the highest specificity and sensitivity – an advantage customers of other chip manufacturers do not have.

Second, the calculated oligonucleotides are produced and purified with strict quality control procedures including MALDI-TOF MS. Huge production capacities, know-how and process automation guarantee high quality and fast service at affordable prices. Moreover, our microarray experts and their cooperation partners do functional validation of each of the catalog arrays. Of course, every individual batch of arrays is quality controlled extensively.

Oligos4Array

The backbone of the array probe design are sophisticated bioinformatics tools such as the Oligos4Array software and our proprietary non-redundant CodeSeq databases. These software tools are part of our unique computational platform called BioGIST® that allows establishment of completely automated workflows; e.g., for oligo probe design and microarray production. Each individual oligo is designed using proprietary design algorithms that ensure absolute gene specificity with one probe per gene.

Oligos4Array – several steps for designing the ideal oligo for every single gene:

1. Design of an oligo probe begins with defining physical parameters such as

• Length
• GC Content
• Secondary structures
• Overlap between selected oligos
• Dimer formation

Extensive R&D efforts proved that 50mers meet the requirements for specificity and sensitivity the best. The default GC content setting is between 40 and 60%, but will be adjusted as required depending on the project. Obviously, the algorithms exclude oligos that show secondary structures, overlaps, and primer dimer formation. Thresholds can be defined individually.

2. Extensive alignments use our non-redundant database CodeSeq to sort out unspecific sequences

In order to find gene specific probes, Oligos4Array compares suggested 50mer sequences with those of all known coding regions of the species of interest (BLAST and Smith-Waterman analysis). For that purpose, a CodeSeq database containing all known coding regions of the respective species is generated (based on redundant public and proprietary databases). As submission of identical sequence information several times to the same public database is quite common today, these databases are redundant information sources. However, only databases that store each sequence once exclusively, i.e., non-redundant databases, can ensure automated high throughput design. The reason is that for efficient comparisons between oligo sequences and sequences stored in databases, the parameter “each oligo sequence is allowed to occur once only” is clear without ambiguity. Therefore, we establish and update regularly our proprietary CodeSeq databases for each organism of interest.

First, all sequences available in public and proprietary databases for a specific organism are clustered, whereby each cluster represents one unique gene. Secondly, a consensus sequence or contig generated from each cluster is entered into our CodeSeq database and thus forms the basis for gene specific and automated oligo probe design.

3. Application dependent selection of gene specific oligonucleotide probes (e.g. exon specific, strain specific or alternative splicing)

4. Recent publications on the ideal length of oligonucleotide probes, as well as experimental evidence from our own research and development indicate that 40-50 mer oligonucleotide probes show an optimal balance of sensitivity and specificity.

Oligo-Production

5. Our laboratory information and management system Biotracker™ controls the fully automated production of the designed oligos in superior quality. Our oligonucleotides are

• Full length products purified from n-1 products and failure products
• Free of salt and metal ions
• Standard QC and identity checked by MALDI-TOF analysis

This constant high quality allows standardized microarray production from batch to batch, and from array to array

6. Complete order process automation and high capacity guarantee an error free and fast service.