Comparative genomics exploration tools

Comparative Genomics focuses on elucidating the genetic differences between different species or different strains of the same species by the comparative analysis of DNA sequences to identify functional elements and regulatory regions. This thesis describes the design and development of two software tools to support comparative genomics research. These tools were specifically developed to support the analysis and assembly of sequence data produced from innovative new DNA sequencing technology from 454 Life Sciences using the PicoTiterPlate(TM) device. This technology will dramatically affect comparative genomics research. Currently available software tools were developed to handle traditional shotgun sequences averaging 500-1000 base pairs in length. These tools are inadequate to handle the unique characteristics of sequence reads generated by 454 Life Sciences. The goal of this research is to adapt currently available tools and develop new tools to be used for sequence reads generated by any sequencing technology, even those having different characteristics from the traditional shotgun sequences

GENtle, a free multi-purpose molecular biology tool

A result of modern techniques in molecular biology, especially DNA sequencing, is the exponentially growing amount of available data. Besides giant, specialized databases, which are accessible over the Internet, all work groups in the field of molecular biology today need to handle, modify, analyze and store sequence information. This trend notwithstanding, general purpose software for these tasks often suffers from severe drawbacks. Free software exists, but is often hard to set up and operate for users on today's point-and-click interfaces, and usually leads to the application of a patch-work of multiple, only partially compatible tools and web services. Commercial software often covers only parts of the required functions, and tends to lock the user into proprietary formats. In my thesis, I have developed GENtle, a free, multi-purpose bioinformatics software, seamlessly integrating diverse applications for every-day lab use in a single package. It was designed for easy and intuitive use, while providing many powerful functions. This C++ application runs on multiple platforms, is optimized for performance, and includes database interfaces for easy sequence management. It features DNA and protein sequence management and analysis, virtual cloning, gels, and PCR, primer design, alignment generation and layout, chromatogram and image display, as well as many related functions. GENtle strives to satisfy the need for an easy and comfortable, yet powerful multi-purpose tool. One design goal of GENtle was "instant responsiveness". Likewise, consistent display and handling are of great importance. GENtle has been outfitted with modules for DNA and protein sequence management, editing, and analysis, primer design, virtual PCR, alignments, virtual gels, a plethora of import and export formats, integrated database management, internet search functionality, an auto-update mechanism, and a number of integrated tools. GENtle is free software licensed under the GPL and available for Windows, Mac OSX, and Linux in several languages. As such, it is already in use in research groups worldwide

The Art of Designing DNA Nanostructures with CAD Software

Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source

Gene Designer: a synthetic biology tool for constructing artificial DNA segments

BACKGROUND: Direct synthesis of genes is rapidly becoming the most efficient way to make functional genetic constructs and enables applications such as codon optimization, RNAi resistant genes and protein engineering. Here we introduce a software tool that drastically facilitates the design of synthetic genes. RESULTS: Gene Designer is a stand-alone software for fast and easy design of synthetic DNA segments. Users can easily add, edit and combine genetic elements such as promoters, open reading frames and tags through an intuitive drag-and-drop graphic interface and a hierarchical DNA/Protein object map. Using advanced optimization algorithms, open reading frames within the DNA construct can readily be codon optimized for protein expression in any host organism. Gene Designer also includes features such as a real-time sliding calculator of oligonucleotide annealing temperatures, sequencing primer generator, tools for avoidance or inclusion of restriction sites, and options to maximize or minimize sequence identity to a reference. CONCLUSION: Gene Designer is an expandable Synthetic Biology workbench suitable for molecular biologists interested in the de novo creation of genetic constructs

Computational and experimental analysis of TAL effector-DNA binding

TAL effectors, from the plant-pathogenic bacterial genus Xanthomonas, are DNA binding proteins that can be engineered to bind to almost any sequence of interest. The DNA target of the TAL effector is encoded by a modular central repeat region, with each repeat specifying a single binding site nucleotide. TAL effectors can be targeted to novel DNA sequences by assembling the corresponding repeat sequence. Therefore, custom TAL effectors have become important tools for manipulating gene expression and creating site-specific DNA modifications. This dissertation explores TAL effector-DNA binding through computational and experimental analyses. I identified positional and composition biases in known TAL effector-target pairs and proposed guidelines for designing custom TAL effectors and TAL effector nucleases (TALENs). Using these guidelines, I created a software tool for TAL effector design. We expanded this tool into a suite of tools for TAL effector/TALEN design and target site prediction. Target site predictions can be used to estimate potential off-target binding of custom TAL effector constructs or to identify unknown targets of natural TAL effectors. Next, I present a case study in engineering disease resist rice plants. Inserting multiple TAL effector binding elements (EBEs) into the promoter of a rice resistance gene conferred resistance to diverse strains of Xanthomonas oryzae. Analysis of the EBE sequences revealed that TAL effectors have evolved to target specific host regulatory sequences, and caution is warranted when introducing such sequences into the promoter of an executor resistance gene. Finally, I examine the role of the TAL effector N terminus in DNA binding. Most natural TAL effector binding sites are preceded by a T at the 5\u27 end (T0). Structural data suggests T0 is encoded by tryptophan 232 (W232) in the cryptic -1st repeat. We show that substitutions for W232 alter TAL effector activity and specificity for T0. However, we find that the TAL effector-T0 interaction is complex and may depend on other residues in the -1st repeat, the 0th cryptic repeat, or repeat sequence context. Better understanding of TAL effector-DNA binding will improve TAL effector design and target prediction and enhance understanding of the role of TAL effectors in plant disease

ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites

<p>Abstract</p> <p>Background</p> <p>Restriction enzymes can produce easily definable segments from DNA sequences by using a variety of cut patterns. There are, however, no software tools that can aid in gene building -- that is, modifying wild-type DNA sequences to express the same wild-type amino acid sequences but with enhanced codons, specific cut sites, unique post-translational modifications, and other engineered-in components for recombinant applications. A fast DNA pattern design algorithm, ICRPfinder, is provided in this paper and applied to find or create potential recognition sites in target coding sequences.</p> <p>Results</p> <p>ICRPfinder is applied to find or create restriction enzyme recognition sites by introducing silent mutations. The algorithm is shown capable of mapping existing cut-sites but importantly it also can generate specified new unique cut-sites within a specified region that are guaranteed not to be present elsewhere in the DNA sequence.</p> <p>Conclusion</p> <p>ICRPfinder is a powerful tool for finding or creating specific DNA patterns in a given target coding sequence. ICRPfinder finds or creates patterns, which can include restriction enzyme recognition sites, without changing the translated protein sequence. ICRPfinder is a browser-based JavaScript application and it can run on any platform, in on-line or off-line mode.</p

Characterization and design of C2H2 zinc finger proteins as custom DNA binding domains

As the storage medium for the source code of life, DNA is fundamentally linked to all cellular processes. Nature employs hundreds of sequence-specific DNA binding proteins as transcription factors and repressors to regulate the flow of genetic expression and replication. By adapting these DNA-binding domains to target desired genome locations, they can be harnessed to treat diseases by regulating genes and repairing diseased gene sequences. The C2H2 zinc finger motif is perhaps the most promising and versatile DNA binding framework. Each C2H2 zinc finger domain (module) is capable of recognizing approximately three adjacent nucleotide bases in standard B form DNA. Through directed mutagenesis, novel zinc finger modules (ZFMs) can be selected for most of the 64 possible DNA triplets. By assembling multiple ZFMs with the appropriate linkers, zinc finger proteins (ZFPs) can be generated to specifically bind extended DNA sequence motifs. Several methods of varying complexity are currently available for ZFP engineering. ZFPs generated from the relatively simple modular design method often fail to function in vivo. Those generated using the most reliable module subsets, those recognizing triplets with a 5\u27 guanine (GNN), only function successfully only an estimated 50% of the time, while modularly assembled ZFPs comprising primarily non-GNN modules rarely function in vivo. These low success rates are extremely problematic for applications requiring multiple ZFPs that target adjacent sequence motifs. More complex ZFP engineering approaches provide enhanced success rates, as compared to modular design, with the drawback that they are also more labor intensive and require additional biological expertise. In this research we developed and engineered novel ZFPs, analyzed characteristics of functional custom zinc finger proteins and their targets, formulated algorithms predictive of ZFP success for both modular assembly and OPEN (Oligomerized Pool Engineering) selection methods, and generated a web-based server and software tools to aid others in the successful application of this technology

Theoretical Design and Analysis of Multivolume Digital Assays with Wide Dynamic Range Validated Experimentally with Microfluidic Digital PCR

This paper presents a protocol using theoretical methods and free software to design and analyze multivolume digital PCR (MV digital PCR) devices; the theory and software are also applicable to design and analysis of dilution series in digital PCR. MV digital PCR minimizes the total number of wells required for “digital” (single molecule) measurements while maintaining high dynamic range and high resolution. In some examples, multivolume designs with fewer than 200 total wells are predicted to provide dynamic range with 5-fold resolution similar to that of single-volume designs requiring 12 000 wells. Mathematical techniques were utilized and expanded to maximize the information obtained from each experiment and to quantify performance of devices and were experimentally validated using the SlipChip platform. MV digital PCR was demonstrated to perform reliably, and results from wells of different volumes agreed with one another. No artifacts due to different surface-to-volume ratios were observed, and single molecule amplification in volumes ranging from 1 to 125 nL was self-consistent. The device presented here was designed to meet the testing requirements for measuring clinically relevant levels of HIV viral load at the point-of-care (in plasma, 1 000 000 molecules/mL), and the predicted resolution and dynamic range was experimentally validated using a control sequence of DNA. This approach simplifies digital PCR experiments, saves space, and thus enables multiplexing using separate areas for each sample on one chip, and facilitates the development of new high-performance diagnostic tools for resource-limited applications. The theory and software presented here are general and are applicable to designing and analyzing other digital analytical platforms including digital immunoassays and digital bacterial analysis. It is not limited to SlipChip and could also be useful for the design of systems on platforms including valve-based and droplet-based platforms. In a separate publication by Shen et al. (J. Am. Chem. Soc., 2011, DOI: 10.1021/ja2060116), this approach is used to design and test digital RT-PCR devices for quantifying RNA

The BiSearch web server

BACKGROUND: A large number of PCR primer-design softwares are available online. However, only very few of them can be used for the design of primers to amplify bisulfite-treated DNA templates, necessary to determine genomic DNA methylation profiles. Indeed, the number of studies on bisulfite-treated templates exponentially increases as determining DNA methylation becomes more important in the diagnosis of cancers. Bisulfite-treated DNA is difficult to amplify since undesired PCR products are often amplified due to the increased sequence redundancy after the chemical conversion. In order to increase the efficiency of PCR primer-design, we have developed BiSearch web server, an online primer-design tool for both bisulfite-treated and native DNA templates. RESULTS: The web tool is composed of a primer-design and an electronic PCR (ePCR) algorithm. The completely reformulated ePCR module detects potential mispriming sites as well as undesired PCR products on both cDNA and native or bisulfite-treated genomic DNA libraries. Due to the new algorithm of the current version, the ePCR module became approximately hundred times faster than the previous one and gave the best performance when compared to other web based tools. This high-speed ePCR analysis made possible the development of the new option of high-throughput primer screening. BiSearch web server can be used for academic researchers at the site. CONCLUSION: BiSearch web server is a useful tool for primer-design for any DNA template and especially for bisulfite-treated genomes. The ePCR tool for fast detection of mispriming sites and alternative PCR products in cDNA libraries and native or bisulfite-treated genomes are the unique features of the new version of BiSearch software

Applications and Challenges of Real-time Mobile DNA Analysis

The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA sequencing outside of laboratory, leading to faster and more accessible DNA-based diagnostics. However, portable DNA sequencing and analysis are challenging for mobile systems, owing to high data throughputs and computationally intensive processing performed in environments with unreliable connectivity and power. In this paper, we provide an analysis of the challenges that mobile systems and mobile computing must address to maximize the potential of portable DNA sequencing, and in situ DNA analysis. We explain the DNA sequencing process and highlight the main differences between traditional and portable DNA sequencing in the context of the actual and envisioned applications. We look at the identified challenges from the perspective of both algorithms and systems design, showing the need for careful co-design