A web service is a service offered by an electronic device to another electronic device, communicating with each other via the World Wide Web. Another common application offered to the end user may be a mashup, where a web server consumes several web services at different machines, the W3C defines a web service generally as, A web service is a software system designed to support interoperable machine-to-machine interaction over a network. Web services may use SOAP over HTTP protocol, allowing less costly interactions over the Internet than via proprietary solutions like EDI/B2B, besides SOAP over HTTP, web services can be implemented on other reliable transport mechanisms like FTP. In a 2002 document, the W3C Web Services Architecture Working Group defined a Web Services Architecture, in this, It has an interface described in a machine-processable format. The term web service describes a way of integrating web-based applications using the XML, SOAP, WSDL. A web service is a method of communication between two electronic devices over a network and it is a software function provided at a network address over the web with the service always on as in the concept of utility computing.
Many organizations use multiple systems for management. Different software systems often need to exchange data with other. The software system that requests data is called a service requester, whereas the system that would process the request. Different software may use different programming languages, and hence there is a need for a method of exchange that doesnt depend upon a particular programming language. Most types of software can, interpret XML tags, web services can use XML files for data exchange. Rules for communication between different systems need to be defined, such as, How one system can request data from another system, which specific parameters are needed in the data request. What would be the structure of the data produced, what error messages to display when a certain rule for communication is not observed, to make troubleshooting easier. All of these rules for communication are defined in a file called WSDL, a directory called UDDI defines which software system should be contacted for which type of data.
So when one software system needs one particular report/data, it would go to the UDDI, once the software system finds out which other system it should contact, it would contact that system using a special protocol called SOAP. The service provider system would first validate the data request by referring to the WSDL file, a Web API is a development in web services where emphasis has been moving to simpler representational state transfer based communications. RESTful APIs do not require XML-based web service protocols to support their interfaces, Automated tools can aid in the creation of a web service. For services using WSDL, it is possible to automatically generate WSDL for existing classes or to generate a class skeleton given existing WSDL
In genetics, complementary DNA is double-stranded DNA synthesized from a single stranded RNA template in a reaction catalyzed by the enzyme reverse transcriptase. CDNA is often used to clone genes in prokaryotes. When scientists want to express a protein in a cell that does not normally express that protein. CDNA is produced naturally by retroviruses and integrated into the hosts genome, the term cDNA is used, typically in a bioinformatics context, to refer to an mRNA transcripts sequence, expressed as DNA bases rather than RNA bases. The number of introns present in a cDNA is zero, since it is derived from eukaryotic mRNA which does not contain introns, although there are several methods for doing so, cDNA is most often synthesized from mature mRNA using the enzyme reverse transcriptase. This enzyme, which occurs in retroviruses, operates on a single strand of mRNA. To obtain eukaryotic cDNA whose introns have been removed, A eukaryotic cell transcribes the DNA into RNA, the same cell processes the pre-mRNA strands by removing introns, and adding a poly-A tail and 5’ Methyl-Guanine cap This mixture of mature mRNA strands is extracted from the cell.
The Poly-A tail of the post-transcription mRNA can be taken advantage of with oligo beads in an affinity chromatography assay and this synthesizes one complementary strand of DNA hybridized to the original mRNA strand. To synthesize an additional DNA strand, traditionally one would digest the RNA of the strand, using an enzyme like RNase H. After digestion of the RNA, a single stranded DNA is left and because single stranded nucleic acids are hydrophobic and it is likely that the ssDNA forms a hairpin loop at the 3 end. From the hairpin loop, a DNA polymerase can use it as a primer to transcribe a complementary sequence for the ss cDNA. Now, you should be left with a double stranded cDNA with identical sequence as the mRNA of interest, Complementary DNA is often used in gene cloning or as gene probes or in the creation of a cDNA library. Partial sequences of cDNAs are often obtained as expressed sequence tags and this is achieved by designing sequence-specific DNA primers that hybridize to the 5 and 3 ends of a cDNA region coding for a protein.
Once amplified, the sequence can be cut at each end with nucleases, such vectors allow for self-replication, inside the cells, and potentially integration in the host DNA. They typically contain a promoter to drive transcription of the target cDNA into mRNA. Some viruses use cDNA to turn their viral RNA into mRNA, the mRNA is used to make viral proteins to take over the host cell. CDNA library cDNA microarray RNA-Seq H-Invitational Database Functional Annotation of the Mouse database Complementary DNA tool
Nucleic acid sequence
A nucleic acid sequence is a succession of letters that indicate the order of nucleotides within a DNA or RNA molecule. By convention, sequences are presented from the 5 end to the 3 end. For DNA, the strand is used. Because nucleic acids are linear polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is termed the primary structure, the sequence has capacity to represent information. Biological deoxyribonucleic acid represents the information which directs the functions of a living thing, nucleic acids have a secondary structure and tertiary structure. Primary structure is sometimes referred to as primary sequence. Conversely, there is no concept of secondary or tertiary sequence. Nucleic acids consist of a chain of linked units called nucleotides, each nucleotide consists of three subunits, a phosphate group and a sugar make up the backbone of the nucleic acid strand, and attached to the sugar is one of a set of nucleobases.
The nucleobases are important in base pairing of strands to form secondary and tertiary structure such as the famed double helix. The possible letters are A, C, G, and T, in the typical case, the sequences are printed abutting one another without gaps, as in the sequence AAAGTCTGAC, read left to right in the 5 to 3 direction. With regards to transcription, a sequence is on the strand if it has the same order as the transcribed RNA. One sequence can be complementary to sequence, meaning that they have the base on each position in the complementary. For example, the sequence to TTAC is GTAA. If one strand of the double-stranded DNA is considered the sense strand, the other strand, considered the antisense strand, will have the complementary sequence to the sense strand. Apart from adenine, guanine and uracil, in DNA, the most common modified base is 5-methylcytidine. In RNA, there are many modified bases, including pseudouridine, inosine, ribothymidine and 7-methylguanosine and xanthine are two of the many bases created through mutagen presence, both of them through deamination.
Hypoxanthine is produced from adenine, xanthine from guanine, deamination of cytosine results in uracil
A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases and this is reported as a text string, called a read. Some DNA sequencers can be considered optical instruments as they analyze light signals originating from fluorochromes attached to nucleotides, the first automated DNA sequencer, invented by Lloyd M. Smith, was introduced by Applied Biosystems in 1987. It used the Sanger sequencing method, a technology which formed the basis of the “first generation” of DNA sequencers and this first generation of DNA sequencers are essentially automated electrophoresis systems that detect the migration of labelled DNA fragments. Therefore, these sequencers can be used in the genotyping of genetic markers where only the length of a DNA fragment needs to be determined. The Human Genome Project catalysed the development of cheaper, high throughput and these include the 454, SOLiD and Illumina DNA sequencing platforms.
Next generation sequencing machines have increased the rate of DNA sequence substantially compared with previous Sanger methods, DNA samples can be prepared automatically in as little as 90 mins, while a human genome can be sequenced at 15 times coverage in a matter of days. More recent, third-generation DNA sequencers such as SMRT and Oxford Nanopore measure the addition of nucleotides to a single DNA molecule in real time. Because of limitations in DNA sequencer technology these reads are compared to the length of a genome therefore the reads must be assembled into longer contigs. The data may contain errors, caused by limitations in the DNA sequencing technique or by errors during PCR amplification. DNA sequencer manufacturers use a number of different methods to detect which DNA bases are present, the specific protocols applied in different sequencing platforms have an impact in the final data that is generated. Therefore, comparing data quality and cost across different technologies can be a daunting task, each manufacturer provides their own ways to inform sequencing errors and scores.
However and scores between different platforms cannot always be compared directly, since these systems rely on different DNA sequencing approaches, choosing the best DNA sequencer and method will typically depend on the experiment objectives and available budget. The first DNA sequencing methods were developed by Gilbert and Sanger, Gilbert introduced a sequencing method based on chemical modification of DNA followed by cleavage at specific bases whereas Sanger’s technique is based on dideoxynucleotide chain termination. The Sanger method became popular due to its efficiency and low radioactivity. The first automated DNA sequencer was the AB370A, introduced in 1986 by Applied Biosystems, the AB370A was able to sequence 96 samples simultaneously,500 kilobases per day, and reaching read lengths up to 600 bases. The next major advance was the release in 1995 of the AB310 which utilized a linear polymer in a capillary in place of the gel for DNA strand separation by electrophoresis. These techniques formed the base for the completion of the human genome project in 2001, the human genome project catalysed the development of cheaper, high throughput and more accurate platforms known as Next Generation Sequencers
European Bioinformatics Institute
The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory. The original goal was to establish a computer database of DNA sequences. The task grew in scale with the start of the genome projects and it soon became apparent that the EMBL Nucleotide Sequence Data Library needed better financial security to ensure its long-term viability and to cope with the sheer scale of the task. There was a need for research and development to provide services, to collaborate with partners to support the project. From 1992 through to 1994, a transition of the activities in Heidelberg took place. When the EMBL-EBI moved to Hinxton it hosted two databases, one for nucleotide sequences and one for protein sequences, since then, the EMBL-EBI has diversified to provide data resources in all the major molecular domains and expanded to include a broad research base. It provides user support and offers advanced training in bioinformatics, since 2013, EMBL-EBI has been listed as a data and service provider in the Registry of Research Data Repositories.
As part of EMBL, the largest part of EMBL-EBIs funding comes from the governments of EMBLs 21 member states. Other major funders include the European Commission, Wellcome Trust, US National Institutes of Health, UK Research Councils, EMBL-EBIs industry partners and the UK Department of Trade and Industry. In addition, the Wellcome Trust provides the facilities for the EMBL-EBI on its Genome Campus at Hinxton, the EMBL-EBI hosts a number of publicly open, free to use life science resources, including biomedical databases, analysis tools and bio-ontologies
The Internet is the global system of interconnected computer networks that use the Internet protocol suite to link devices worldwide. The origins of the Internet date back to research commissioned by the United States federal government in the 1960s to build robust, the primary precursor network, the ARPANET, initially served as a backbone for interconnection of regional academic and military networks in the 1980s. Although the Internet was widely used by academia since the 1980s, Internet use grew rapidly in the West from the mid-1990s and from the late 1990s in the developing world. In the two decades since then, Internet use has grown 100-times, measured for the period of one year, newspaper and other print publishing are adapting to website technology, or are reshaped into blogging, web feeds and online news aggregators. The entertainment industry was initially the fastest growing segment on the Internet, the Internet has enabled and accelerated new forms of personal interactions through instant messaging, Internet forums, and social networking.
Business-to-business and financial services on the Internet affect supply chains across entire industries, the Internet has no centralized governance in either technological implementation or policies for access and usage, each constituent network sets its own policies. The term Internet, when used to refer to the global system of interconnected Internet Protocol networks, is a proper noun. In common use and the media, it is not capitalized. Some guides specify that the word should be capitalized when used as a noun, the Internet is often referred to as the Net, as a short form of network. Historically, as early as 1849, the word internetted was used uncapitalized as an adjective, the designers of early computer networks used internet both as a noun and as a verb in shorthand form of internetwork or internetworking, meaning interconnecting computer networks. The terms Internet and World Wide Web are often used interchangeably in everyday speech, the World Wide Web or the Web is only one of a large number of Internet services.
The Web is a collection of interconnected documents and other web resources, linked by hyperlinks, the term Interweb is a portmanteau of Internet and World Wide Web typically used sarcastically to parody a technically unsavvy user. The ARPANET project led to the development of protocols for internetworking, the third site was the Culler-Fried Interactive Mathematics Center at the University of California, Santa Barbara, followed by the University of Utah Graphics Department. In an early sign of growth, fifteen sites were connected to the young ARPANET by the end of 1971. These early years were documented in the 1972 film Computer Networks, early international collaborations on the ARPANET were rare. European developers were concerned with developing the X.25 networks, in December 1974, RFC675, by Vinton Cerf, Yogen Dalal, and Carl Sunshine, used the term internet as a shorthand for internetworking and RFCs repeated this use. Access to the ARPANET was expanded in 1981 when the National Science Foundation funded the Computer Science Network, in 1982, the Internet Protocol Suite was standardized, which permitted worldwide proliferation of interconnected networks.5 Mbit/s and 45 Mbit/s.
Commercial Internet service providers emerged in the late 1980s and early 1990s, the ARPANET was decommissioned in 1990
Consortium is a Latin word, meaning partnership, association or society and derives from consors partner, itself from con- together and sors fate, meaning owner of means or comrade. The Big Ten Academic Alliance and Five Colleges, Inc. along with the Claremont Consortium are among the oldest and most successful higher education consortia in the United States. The Big Ten Academic Alliance, formerly known as the Committee on Institutional Cooperation, the participants in Five Colleges, Inc. are, Amherst College, Hampshire College, Mount Holyoke College, Smith College, and the University of Massachusetts Amherst. Another example of a successful consortium is the Five Colleges of Ohio of Ohio, Oberlin College, Ohio Wesleyan University, Kenyon College, College of Wooster and Denison University. These consortia have pooled the resources of their colleges and the universities to share human and material assets as well as to link academic. An example of a non-profit consortium is the Appalachian College Association located in Richmond, the association consists of 35 private liberal arts colleges and universities spread across the central Appalachian mountains in Kentucky, North Carolina, Tennessee and West Virginia.
Collectively these higher education institutions serve approximately 42,500 students, six research universities in the region are affiliated with the ACA. These institutions assist the ACA in reviewing grant and fellowship applications, conducting workshops, the ACA works to serve higher education in the rural regions of these five states. An example of a for-profit consortium is a group of banks that collaborate to make a loan—also known as a syndicate and this type of loan is more commonly known as a syndicated loan. In England it is common for a consortium to buy out financially struggling football clubs in order to them out of liquidation. Hulu, the American video streaming service, is owned by a consortium of media conglomerates including Time Warner, 21st Century Fox, Comcast. Airbus Industries was formed in 1970 as a consortium of aerospace manufacturers, the retention of production and engineering assets by the partner companies in effect made Airbus Industries a sales and marketing company.
This arrangement led to inefficiencies due to the inherent conflicts of interest that the four partner companies faced, the companies collaborated on development of the Airbus range, but guarded the financial details of their own production activities and sought to maximize the transfer prices of their sub-assemblies. In 2001, EADS and BAE Systems transferred their Airbus production assets to a new company, in return, they got 80% and 20% shares respectively. BAE would sell its share to EADS, coopetition is a word coined from cooperation and competition. It is used when companies otherwise competitors collaborate in a consortium to cooperate on areas non-strategic for their core businesses and they prefer to reduce their costs on these non-strategic areas and compete on other areas where they can differentiate better. For example, the GENIVI Alliance is a consortium between different car makers in order to ease building an in-vehicle infotainment system. Another example is the World Wide Web Consortium, which is a consortium that standardizes web technologies like HTML, XML, joint venture This article incorporates text from a publication now in the public domain, Charles, ed. passim
Whole genome sequencing
Whole genome sequencing is the process of determining the complete DNA sequence of an organisms genome at a single time. This entails sequencing all of an organisms chromosomal DNA as well as DNA contained in the mitochondria and, for plants, whole genome sequencing has largely been used as a research tool, but is currently being introduced to clinics. In the future of personalized medicine, whole genome sequence data will be an important tool to guide therapeutic intervention, in addition, whole genome sequencing should not be confused with methods that sequence specific subsets of the genome - such methods include whole exome sequencing or SNP genotyping. Almost all truly complete genomes are of microbes, the full genome is thus sometimes used loosely to mean greater than 95%. The remainder of this focuses on nearly complete human genomes. The DNA sequencing methods used in the 1970s and 1980s were manual, for example Maxam-Gilbert sequencing, the shift to more rapid, automated sequencing methods in the 1990s finally allowed the sequence of whole genomes.
The first organism to have its genome sequenced was Haemophilus influenzae in 1995. After it, the genomes of bacteria and some archaea were first sequenced. H. influenzae has a genome of 1,830,140 base pairs of DNA, in contrast, both unicellular and multicellular such as Amoeba dubia and humans respectively, have much larger genomes. Amoeba dubia has a genome of 700 billion nucleotide pairs spread across thousands of chromosomes, humans contain fewer nucleotide pairs than A. dubia however their genome size far outweighs the genome size of individual bacteria. The first bacterial and archaeal genomes, including that of H. influenzae, were sequenced by Shotgun sequencing, in 1996 the first eukaryotic genome was sequenced. S. cerevisiae, an organism in biology has a genome of only around 12 million nucleotide pairs. The first multicellular eukaryote, and animal, to have its genome sequenced was the nematode worm. In 1999, the entire DNA sequence of human chromosome 22, by the year 2000, the second animal and second invertebrate genome was sequenced - that of the fruit fly Drosophila melanogaster - a popular choice of model organism in experimental research.
The first plant genome - that of the model organism Arabidopsis thaliana - was fully sequenced by 2000, by 2001, a draft of the entire human genome sequence was published. The genome of the laboratory mouse Mus musculus was completed in 2002, in 2004, the Human Genome Project published the human genome. Currently, thousands of genomes have been sequenced, almost any biological sample containing a full copy of the DNA—even a very small amount of DNA or ancient DNA—can provide the genetic material necessary for full genome sequencing. Such samples may include saliva, epithelial cells, bone marrow, seeds, plant leaves, the genome sequence of a single cell selected from a mixed population of cells can be determined using techniques of single cell genome sequencing
Developed by Frederick Sanger and colleagues in 1977, it was the most widely used sequencing method for approximately 39 years. More recently, higher volume Sanger sequencing has been supplanted by Next-Gen sequencing methods, especially for large-scale, the Sanger method remains in wide use, for smaller-scale projects, validation of Next-Gen results and for obtaining especially long contiguous DNA sequence reads. The ddNTPs may be radioactively or fluorescently labeled for detection in automated sequencing machines, the DNA sample is divided into four separate sequencing reactions, containing all four of the standard deoxynucleotides and the DNA polymerase. To each reaction is added one of the four dideoxynucleotides. Putting it in a more sensible order, four reactions are needed in this process to test all four ddNTPs. Following rounds of template DNA extension from the primer, the resulting DNA fragments are heat denatured and separated by size using gel electrophoresis. In the original publication of 1977, the formation of base-paired loops of ssDNA was a cause of difficulty in resolving bands at some locations.
This is frequently performed using a denaturing polyacrylamide-urea gel with each of the four reactions run in one of four individual lanes, the DNA bands may be visualized by autoradiography or UV light and the DNA sequence can be directly read off the X-ray film or gel image. In the image on the right, X-ray film was exposed to the gel, a dark band in a lane indicates a DNA fragment that is the result of chain termination after incorporation of a dideoxynucleotide. The relative positions of the different bands among the four lanes, dye-primer sequencing facilitates reading in an optical system for faster and more economical analysis and automation. The development by Leroy Hood and coworkers of fluorescently labeled ddNTPs and primers set the stage for automated, chain-termination methods have greatly simplified DNA sequencing. For example, chain-termination-based kits are available that contain the reagents needed for sequencing, pre-aliquoted. Limitations include non-specific binding of the primer to the DNA, affecting accurate read-out of the DNA sequence, dye-terminator sequencing utilizes labelling of the chain terminator ddNTPs, which permits sequencing in a single reaction, rather than four reactions as in the labelled-primer method.
In dye-terminator sequencing, each of the four dideoxynucleotide chain terminators is labelled with fluorescent dyes, owing to its greater expediency and speed, dye-terminator sequencing is now the mainstay in automated sequencing. This problem has been addressed with the use of modified DNA polymerase enzyme systems and dyes that minimize incorporation variability, the dye-terminator sequencing method, along with automated high-throughput DNA sequence analyzers, is now being used for the vast majority of sequencing projects. Automated DNA-sequencing instruments can sequence up to 384 DNA samples in a single batch, batch runs may occur up to 24 times a day. DNA sequencers separate strands by using capillary electrophoresis, they detect and record dye fluorescence. Sequencing reactions, cleanup and re-suspension of samples in a solution are performed separately
Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism and to annotate protein-coding genes and other important genome-encoded features. The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism, for a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, in a shotgun sequencing project, all the DNA from a source is first fractured into millions of small pieces. These pieces are read by automated sequencing machines, which can read up to 1000 nucleotides or bases at a time. A genome assembly algorithm works by taking all the pieces and aligning them to one another and these overlapping reads can be merged, and the process continues. Genome assembly is a very difficult problem, made more difficult because many genomes contain large numbers of identical sequences.
These repeats can be thousands of long, and some occur in thousands of different locations, especially in the large genomes of plants. The resulting genome sequence is produced by combining the information sequenced contigs, scaffolds are positioned along the physical map of the chromosomes creating a golden path. Originally, most large-scale DNA sequencing centers developed their own software for assembling the sequences that they produced, this has changed as the software has grown more complex and as the number of sequencing centers has increased. Since the 1980s, molecular biology and bioinformatics have created the need for DNA annotation, when sequencing a genome, there are usually regions that are difficult to sequence. Thus, completed genome sequences are rarely ever complete, and terms such as working draft or essentially complete have been used to accurately describe the status of such genome projects. Even when every pair of a genome sequence has been determined. It could be argued that a complete genome project should include the sequences of mitochondria and it is often reported that the goal of sequencing a genome is to obtain information about the complete set of genes in that particular genome sequence.
The proportion of a genome that encodes for genes may be very small, however, it is not always possible to only sequence the coding regions separately. In many ways genome projects do not confine themselves to only determining a DNA sequence of an organism, such projects may include gene prediction to find out where the genes are in a genome, and what those genes do. There may be related projects to sequence ESTs or mRNAs to help out where the genes actually are. Historically, when sequencing eukaryotic genomes it was common to first map the genome to provide a series of landmarks across the genome, rather than sequence a chromosome in one go, it would be sequenced piece by piece. Changes in technology and in improvements to the processing power of computers
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence Database Collaboration, the National Center for Biotechnology Information is a part of the National Institutes of Health in the United States. GenBank and its collaborators receive sequences produced in laboratories throughout the world more than 100,000 distinct organisms. GenBank continues to grow at a rate, doubling every 18 months. Release 194, produced in February 2013, contained over 150 billion nucleotide bases in more than 162 million sequences, GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers. Only original sequences can be submitted to GenBank, direct submissions are made to GenBank using BankIt, which is a Web-based form, or the stand-alone submission program, Sequin.
Upon receipt of a submission, the GenBank staff examines the originality of the data and assigns an accession number to the sequence. The submissions are released to the database, where the entries are retrievable by Entrez or downloadable by FTP. Bulk submissions of Expressed Sequence Tag, Sequence-tagged site, Genome Survey Sequence, the GenBank direct submissions group processes complete microbial genome sequences. Funding was provided by the National Institutes of Health, the National Science Foundation, the Department of Energy, LANL collaborated on GenBank with the firm Bolt and Newman, and by the end of 1983 more than 2,000 sequences were stored in it. In the mid 1980s, the Intelligenetics bioinformatics company at Stanford University managed the GenBank project in collaboration with LANL, as one of the earliest bioinformatics community projects on the Internet, the GenBank project started BIOSCI/Bionet news groups for promoting open access communications among bioscientists. During 1989 to 1992, the GenBank project transitioned to the newly created National Center for Biotechnology Information, the GenBank release notes for release 162.0 state that from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months.
As of 15 June 2016, GenBank release 214.0 has 194,463,572 loci,213,200,907,819 bases, from 194,463,572 reported sequences. The GenBank database includes data sets that are constructed mechanically from the main sequence data collection. On the other hand, while commercial databases potentially contain high-quality filtered sequence data, the results showed that analyses performed using GenBank combined with EzTaxon-e were more discriminative than using GenBank or other databases alone. GenBank Example sequence record, for hemoglobin beta BankIt Sequin — a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database. EMBOSS — free, open source software for molecular biology GenBank, RefSeq, TPA and UniProt, Whats in a Name