What is encode?

In computers, encoding is the process of putting a sequence of characters (letters, numbers, punctuation, and certain…

symbols) into a specialized format for efficient transmission or storage. Decoding is the opposite process — the conversion of an encoded format back into the original sequence of characters. Encoding and decoding are used in data communications, networking, and storage. The term is especially applicable to radio (wireless) communications systems.

The code used by most computers for text files is known as ASCII (American Standard Code for Information Interchange, pronounced ASK-ee). ASCII can depict uppercase and lowercase alphabetic characters, numerals, punctuation marks, and common symbols. Other commonly-used codes include Unicode, BinHex, Uuencode, and MIME.

In data communications, Manchester encoding is a special form of encoding in which the binary digits (bits) represent the transitions between high and low logic states. In radio communications, numerous encoding and decoding methods exist, some of which are used only by specialized groups of people (amateur radio operators, for example).

The oldest code of all, originally employed in the landline telegraph during the 19th century, is the Morse code.

The terms encoding and decoding are often used in reference to the processes of analog-to-digital conversion and digital-to-analog conversion.

In this sense, these terms can apply to any form of data, including text, images, audio, video, multimedia, computer programs, or signals in sensors, telemetry, and control systems.

Encoding should not be confused with encryption, a process in which data is deliberately altered so as to conceal its content. Encryption can be done without changing the particular code that the content is in, and encoding can be done without deliberately concealing the content.

  • What is ENCODE?
  • What is ENCODE?
  • What is ENCODE?
  • What is ENCODE?
  • What is ENCODE? Margaret Rouse asks:

    What type of text encoding do you use – ASCII, Unicode, MIME or something else?

ENCODE

What is ENCODE?ENCODEContentDescriptionWhole-genome databaseContactResearch centerStanford UniversityLaboratoryStanford Genome Technology Center: Cherry Lab; Formerly: University of California, Santa CruzAuthorsCricket Alicia Sloan[1]Primary citationPMID 26980513Release date2010 (2010)AccessWebsiteencodeproject.org

The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims to identify functional elements in the human genome.

History

Encode was launched by the US National Human Genome Research Institute (NHGRI) in September 2003.[2][3][4][5][6] Intended as a follow-up to the Human Genome Project, the ENCODE project aims to identify all functional elements in the human genome.

The project involves a worldwide consortium of research groups, and data generated from this project can be accessed through public databases. The project is beginning its fourth phase as of February 2017.[7]

Motivation and Significance

Humans are estimated to have approximately 20,000 protein-coding genes, which account for about 1.5% of DNA in the human genome.

The primary goal of the ENCODE project is to determine the role of the remaining component of the genome, much of which was traditionally regarded as “junk.

” The activity and expression of protein-coding genes can be modulated by the regulome – a variety of DNA elements, such as promoters, transcriptional regulatory sequences, and regions of chromatin structure and histone modification.

It is thought that changes in the regulation of gene activity can disrupt protein production and cell processes and result in disease. Determining the location of these regulatory elements and how they influence gene transcription could reveal links between variations in the expression of certain genes and the development of disease.[8]

ENCODE is also intended as a comprehensive resource to allow the scientific community to better understand how the genome can affect human health, and to “stimulate the development of new therapies to prevent and treat these diseases”.[3]

The ENCODE Consortium

The ENCODE Consortium is composed primarily of scientists who were funded by US National Human Genome Research Institute (NHGRI). Other participants contributing to the project are brought up into the Consortium or Analysis Working Group.

The pilot phase consisted of eight research groups and twelve groups participating in the ENCODE Technology Development Phase. After 2007, the number of participants grew up to 440 scientists from 32 laboratories worldwide as the pilot phase was officially over. At the moment the consortium consists of different centers which perform different tasks.

ENCODE is a member of the International Human Epigenome Consortium (IHEC).[9]

The ENCODE Project

ENCODE is currently implemented in four phases: the pilot phase and the technology development phase, which were initiated simultaneously;[10] and the production phase. The fourth phase is a continuation of the third, and includes functional characterization and further integrative analysis for the encyclopedia.

The goal of the pilot phase was to identify a set of procedures that, in combination, could be applied cost-effectively and at high-throughput to accurately and comprehensively characterize large regions of the human genome.

The pilot phase had to reveal gaps in the current set of tools for detecting functional sequences, and was also thought to reveal whether some methods used by that time were inefficient or unsuitable for large-scale utilization.

Some of these problems had to be addressed in the ENCODE technology development phase, which aimed to devise new laboratory and computational methods that would improve our ability to identify known functional sequences or to discover new functional genomic elements.

The results of the first two phases determined the best path forward for analyzing the remaining 99% of the human genome in a cost-effective and comprehensive production phase.[3]

The ENCODE Phase I Project: The Pilot Project

The pilot phase tested and compared existing methods to rigorously analyze a defined portion of the human genome sequence.

It was organized as an open consortium and brought together investigators with diverse backgrounds and expertise to evaluate the relative merits of each of a diverse set of techniques, technologies and strategies.

See also:  The science of fire

The concurrent technology development phase of the project aimed to develop new high throughput methods to identify functional elements. The goal of these efforts was to identify a suite of approaches that would allow the comprehensive identification of all the functional elements in the human genome.

Through the ENCODE pilot project, National Human Genome Research Institute (NHGRI) assessed the abilities of different approaches to be scaled up for an effort to analyse the entire human genome and to find gaps in the ability to identify functional elements in genomic sequence.

The ENCODE pilot project process involved close interactions between computational and experimental scientists to evaluate a number of methods for annotating the human genome.

A set of regions representing approximately 1% (30 Mb) of the human genome was selected as the target for the pilot project and was analyzed by all ENCODE pilot project investigators.

All data generated by ENCODE participants on these regions was rapidly released into public databases.[5][11]

Target Selection

For use in the ENCODE pilot project, defined regions of the human genome – corresponding to 30Mb, roughly 1% of the total human genome – were selected. These regions served as the foundation on which to test and evaluate the effectiveness and efficiency of a diverse set of methods and technologies for finding various functional elements in human DNA.

Prior to embarking upon the target selection, it was decided that 50% of the 30Mb of sequence would be selected manually while the remaining sequence would be selected randomly.

The two main criteria for manually selected regions were: 1) the presence of well-studied genes or other known sequence elements, and 2) the existence of a substantial amount of comparative sequence data. A total of 14.

82Mb of sequence was manually selected using this approach, consisting of 14 targets that range in size from 500kb to 2Mb.

The Encyclopedia of DNA Elements (ENCODE)

What is ENCODE?

ENCODE is a public research consortium aimed at identifying all functional elements in the human and mouse genomes.

ENCODE has produced vast amounts of data that can be accessed through the project's freely accessible database, the ENCODE Portal. The ENCODE “Encyclopedia” organizes these data into two levels of annotations: 1) integrative-level annotations, including a registry of candidate cis-regulatory elements and 2) ground-level annotations derived directly from experimental data.

As a result of outreach and collaboration, ENCODE data are widely used. Lists of publications using ENCODE resources can be found on the ENCODE Portal. (See ENCODE-funded Publications and Community Publications.

) The ENCODE Portal also hosts data from modENCODE as well as data from the RoadMap Epigenomics and Genomics of Gene Regulation projects.

Additional information about data standards and guidelines and uniform data processing can also be found on the ENCODE Portal.

The ENCODE Project started in 2003 with the ENCODE Pilot Project, which focused on 1% of the human genome and subsequently completed two additional phases (ENCODE 2 and ENCODE 3) which conducted whole-genome analyses on the human and mouse genomes. A parallel effort was devoted to whole-genome analyses of the C. elegans and D.

melanogaster genomes under the modENCODE Project. In recognition of the need for new approaches, methods and technologies to achieve the goals of ENCODE, NHGRI has also funded four rounds of technology development initiatives since 2003.

A number of these efforts have been incorporated into subsequent phases of ENCODE data production and analysis.

With the success of these three phases of the ENCODE Project and the recognition that additional effort was needed to complete and understand the catalog of candidate regulatory elements compiled, NHGRI funded the fourth phase of ENCODE (ENCODE 4) in February 2017 to continue and expand on its work to understand the human and mouse genomes.

  • Overview ENCODE has produced vast amounts of data that can be accessed through the project's freely accessible database, the ENCODE Portal. The ENCODE “Encyclopedia” organizes these data into two levels of annotations: 1) integrative-level annotations, including a registry of candidate cis-regulatory elements and 2) ground-level annotations derived directly from experimental data. As a result of outreach and collaboration, ENCODE data are widely used. Lists of publications using ENCODE resources can be found on the ENCODE Portal. (See ENCODE-funded Publications and Community Publications.) The ENCODE Portal also hosts data from modENCODE as well as data from the RoadMap Epigenomics and Genomics of Gene Regulation projects. Additional information about data standards and guidelines and uniform data processing can also be found on the ENCODE Portal. The ENCODE Project started in 2003 with the ENCODE Pilot Project, which focused on 1% of the human genome and subsequently completed two additional phases (ENCODE 2 and ENCODE 3) which conducted whole-genome analyses on the human and mouse genomes. A parallel effort was devoted to whole-genome analyses of the C. elegans and D. melanogaster genomes under the modENCODE Project. In recognition of the need for new approaches, methods and technologies to achieve the goals of ENCODE, NHGRI has also funded four rounds of technology development initiatives since 2003. A number of these efforts have been incorporated into subsequent phases of ENCODE data production and analysis. With the success of these three phases of the ENCODE Project and the recognition that additional effort was needed to complete and understand the catalog of candidate regulatory elements compiled, NHGRI funded the fourth phase of ENCODE (ENCODE 4) in February 2017 to continue and expand on its work to understand the human and mouse genomes.
See also:  How to work with negative exponents

ENCODE 4 seeks to expand the catalog of candidate regulatory elements in the human and mouse genomes through the study of a broader diversity of biological samples including those associated with disease as well as by employing novel assays not used previously in ENCODE.

To maximize access to ENCODE data by the research community, all data is shared in databases without controlled access. All newly obtained human biological samples are consented for unrestricted data sharing.

  To study the biological function of candidate regulatory elements already compiled by ENCODE, a new component, functional element characterization, has been added in ENCODE 4.

ENCODE 4 includes the following components:

  • Functional Element Mapping Centers
    • Conduct high-throughput experiments that map biochemical activities to identify candidate functional elements in the human and mouse genomes.
  • Functional Element Characterization Centers
    • Develop and apply generalizable approaches to characterize the role of candidate functional elements in specific biological contexts.
  • Computational Analysis Groups
    • Pilot new applications of ENCODE data
  • Data Coordination Center (DCC)
    • Processes and shares ENCODE metadata and data, and provide a portal for the community to visualize and download data.
  • Data Analysis Center (DAC)
    • Specifies data processing pipelines and quality metrics for major data types, design and perform integrative analysis of ENCODE data to update and refine the Encyclopedia.

Read about the ENCODE Pilot Project.

  • ENCODE 4

    ENCODE 4 seeks to expand the catalog of candidate regulatory elements in the human and mouse genomes through the study of a broader diversity of biological samples including those associated with disease as well as by employing novel assays not used previously in ENCODE.

    To maximize access to ENCODE data by the research community, all data is shared in databases without controlled access. All newly obtained human biological samples are consented for unrestricted data sharing.

      To study the biological function of candidate regulatory elements already compiled by ENCODE, a new component, functional element characterization, has been added in ENCODE 4.

    ENCODE 4 includes the following components:

    • Functional Element Mapping Centers
      • Conduct high-throughput experiments that map biochemical activities to identify candidate functional elements in the human and mouse genomes.
    • Functional Element Characterization Centers
      • Develop and apply generalizable approaches to characterize the role of candidate functional elements in specific biological contexts.
    • Computational Analysis Groups
      • Pilot new applications of ENCODE data
    • Data Coordination Center (DCC)
      • Processes and shares ENCODE metadata and data, and provide a portal for the community to visualize and download data.
    • Data Analysis Center (DAC)
      • Specifies data processing pipelines and quality metrics for major data types, design and perform integrative analysis of ENCODE data to update and refine the Encyclopedia.

    Read about the ENCODE Pilot Project.

Grantees Institutions Title Grant Number
Mapping Awards
Bradley Bernstein Chad Nusbaum Broad Institute of Harvard and MIT A Catalog of Cell Types and Genomic Elements in Tissues, Organoids and Disease UM1 HG009390
Erez Lieberman Aiden Baylor College of Medicine Genome-Wide Mapping of Loops Using In Situ Hi-C UM1 HG009375
Mats Ljungman University of Michigan Mapping of Novel Candidate Functional Elements with Bru-Seq Technology UM1 HG009382
Richard Myers Eric Mendenhall HudsonAlpha Institute for Biotechnology University of Alabama in Huntsville

What Is ENCODE, and Why Does It Matter?

A giant leap has just been taken in humanity's understanding of itself. That leap is called ENCODE. Here's what you need to know.

Eleven years ago, scientists sequenced the human genome. That is, they unraveled the spirals of DNA packed inside the nucleus of each of our cells and figured out the ordering of its 3.3 billion chemical “base pairs,” or the molecular letters, of sorts, that spell out instructions for the cells to follow.

But although the Human Genome Project (as the endeavor was called) established the order of the base pairs, most of the code that these letters spelled out remained encrypted.

Scientists could see that roughly 23,000 sections of the genome, made up of about 1,000 base pairs each, coded for proteins.

In other words, these sections, called genes, were structured in such a way that cells could read them off to build protein molecules, which then performed cellular functions. But the genes made up less than 2 percent of the total human genome.

What did the rest of the endless spirals of DNA base pairs mean? Many scientists thought most of it was useless gobbledygook left over from our evolutionary past. They called it “junk DNA.” [How to Speak Genetics: A Glossary]

Now, an international collaboration of 442 scientists has unveiled the Encyclopedia of DNA Elements, nicknamed ENCODE.

In more than two dozen articles published in Nature, Science and other journals, the scientists present nine years of research showing that genes are just one element of a long “parts list” that makes up the human genome.

Rather than being mostly junk, 80 percent of DNA has a function, and ENCODE is the encyclopedia that describes what all of it does.

Half or more of human DNA acts as “gene switches.” These portions of code control when genes turn on and off, affecting how many proteins get built both throughout the day and over the course of a lifetime.

There's a gene switch that tells an undifferentiated cell in an embryo to develop into a liver cell, for example; there's another switch that directs a cell in the pancreas to rev up its insulin production after a meal; and there's another that tells a skin cell it's time to bud off, notes Time Magazine.

  • “What we learned from ENCODE is how complicated the human genome is, and the incredible choreography that is going on with the immense number of switches that are choreographing how genes are used,” Eric Green, director of the National Human Genome Research Institute (which ran the nine-year-long ENCODE project), told reporters during a teleconference.
  • So, why does it matter that we now have an encyclopedia of human DNA?
  • For one, knowing what so much more of the genetic code actually does will help pinpoint what makes us human; evolutionary biologists can study how the gene switches, as well as the genes, of Homo sapiens diverged from those of other animals.
See also:  Compound possession

More importantly, scientists say the new encyclopedia of DNA will tremendously accelerate our understanding of why diseases occur and how to prevent them. That's because, more often than not, diseases stem from changes that occur in regions of the genetic code formerly labeled “junk.”

“Most of the changes that affect disease don't lie in the genes themselves; they lie in the switches,” Michael Snyder, an ENCODE researcher based at Stanford University, told The New York Times.

Take cancer. It turns out that most of the changes to DNA that make cells turn cancerous do not occur in genes, but in the portions of DNA that exert control over genes: the switches.

Knowing what these switches do, researchers say they can begin to develop drugs that target the control circuitry, rather than targeting the genes themselves, which, in many cases, are impervious to direct attack.

The ENCODE project “will definitely have an impact on our medical research on cancer,” Dr. Mark Rubin, a prostate cancer genomics researcher at Weill Cornell Medical College, told the Times. [What If We Eradicated All Disease?]

What is the Encyclopedia of DNA Elements (ENCODE) Project?

The ENCODE Project was planned as a follow-up to the Human Genome Project. The Human Genome Project sequenced the DNA that makes up the human genome; the ENCODE Project seeks to interpret this sequence. Coinciding with the completion of the Human Genome Project in 2003, the ENCODE Project began as a worldwide effort involving more than 30 research groups and more than 400 scientists.

The approximately 20,000 genes that provide instructions for making proteins account for only about 1 percent of the human genome.

Researchers embarked on the ENCODE Project to figure out the purpose of the remaining 99 percent of the genome.

Scientists discovered that more than 80 percent of this non-gene component of the genome, which was once considered “junk DNA,” actually has a role in regulating the activity of particular genes (gene expression).

Researchers think that changes in the regulation of gene activity may disrupt protein production and cell processes and result in disease. A goal of the ENCODE Project is to link variations in the expression of certain genes to the development of disease.

The ENCODE Project has given researchers insight into how the human genome functions. As researchers learn more about the regulation of gene activity and how genes are expressed, the scientific community will be able to better understand how the entire genome can affect human health.

Encoding

Encoding is the process of converting data from one form to another. While “encoding” can be used as a verb, it is often used as a noun, and refers to a specific type of encoded data. There are several types of encoding, including image encoding, audio and video encoding, and character encoding.

Media files are often encoded to save disk space. By encoding digital audio, video, and image files, they can be saved in a more efficient, compressed format.

Encoded media files are typically similar in quality to their original uncompressed counterparts, but have much smaller file sizes. For example, a WAVE (.WAV) audio file that is converted to an MP3 (.MP3) file may be 1/10 the size of the original WAVE file. Similarly, an MPEG (.

MPG) compressed video file may only require a fraction of the disk space as the original digital video (.DV) file.

Character encoding is another type of encoding that encodes characters as bytes. Since computers only recognize binary data, text must be represented in a binary form. This is accomplished by converting each character (which includes letters, numbers, symbols, and spaces) into a binary code. Common types of text encoding include ASCII and Unicode.

Whenever data is encoded, it can only be read by a program that supports the correct type of encoding. For audio and video files, this is often accomplished by a codec, which decodes the data in real-time.

Most text editors support multiple types of text encoding, so it is rare to find a text file that will not open in a standard text editor.

However, if a text editor does not support the encoding used in a text document, some or all of the characters may appear as strange symbols rather than the intended text.

Updated: September 23, 2010

https://techterms.com/definition/encoding

This page contains a technical definition of Encoding. It explains in computing terminology what Encoding means and is one of many software terms in the TechTerms dictionary.

All definitions on the TechTerms website are written to be technically accurate but also easy to understand. If you find this Encoding definition to be helpful, you can reference it using the citation links above. If you think a term should be updated or added to the TechTerms dictionary, please email TechTerms!

Be the first to comment

Leave a Reply

Your email address will not be published.


*