DNA&RNA Databases and Tools

Databases

BioSystems

Database that groups biomedical literature, small molecules, and sequence data in terms of biological relationships.

Database of Expressed Sequence Tags (dbEST)

A divison of GenBank that contains short single-pass reads of cDNA (transcript) sequences. dbEST can be searched directly through the Nucleotide EST Database.

Database of Genome Survey Sequences (dbGSS)

A division of GenBank that contains short single-pass reads of genomic DNA. dbGSS can be searched directly through the Nucleotide GSS Database.

GenBank

The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis. GenBank consists of several divisions, most of which can be accessed through the Nucleotide database. The exceptions are the EST and GSS divisions, which are accessed through the Nucleotide EST and Nucleotide GSS databases, respectively.

NCBI Website Search

A database of static NCBI web pages, documentation, and online tools. These pages include such content as specialized online sequence analysis tools, back issues of newsletters, legacy resource description pages, sample code, and other miscellaneous resources. Searching this database is equivalent to a site search tool for the whole NCBI web site. FTP site is not covered.

Nucleotide Database

A collection of nucleotide sequences from several sources, including GenBank, RefSeq, the Third Party Annotation (TPA) database, and PDB. Searching the Nucleotide Database will yield available results from each of its component databases.

PopSet

Database of related DNA sequences that originate from comparative studies: phylogenetic, population, environmental and, to a lesser degree, mutational. Each record in the database is a set of DNA sequences. For example, a population set provides information on genetic variation within an organism, while a phylogenetic set may contain sequences, and their alignment, of a single gene obtained from several related organisms.

Probe

A public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.

Reference Sequence (RefSeq)

A collection of curated, non-redundant genomic DNA, transcript (RNA), and protein sequences produced by NCBI. RefSeqs provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. The RefSeq collection is accessed through the Nucleotide and Protein databases.

Sequence Read Archive (SRA)

The Sequence Read Archive (SRA) stores sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Life Technologies AB SOLiD System® , Helicos Biosciences Heliscope®, Complete Genomics®, and Pacific Biosciences SMRT®

Third Party Annotation (TPA) Database

A database that contains sequences built from the existing primary sequence data in GenBank. The sequences and corresponding annotations are experimentally supported and have been published in a peer-reviewed scientific journal. TPA records are retrieved through the Nucleotide Database.

Trace Archive

A repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects.

Tools

Batch Entrez

Allows you to retrieve records from many Entrez databases by uploading a file of GI or accession numbers from the Nucleotide or Protein databases, or a file of unique identifiers from other Entrez databases. Search results can be saved in various formats directly to a local file on your computer.

BLAST (Basic Local Alignment Search Tool)

Finds regions of local similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as to help identify members of gene families.

E-Utilities

Tools that provide access to data within NCBI's Entrez system outside of the regular web query interface. They provide a method of automating Entrez tasks within software applications. Each utility performs a specialized retrieval task, and can be used simply by writing a specially formatted URL.

Genome Workbench

An integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix these data with your own data.

Influenza Virus

Presents data from the NIAID Influenza Genome Sequencing Project and from GenBank, and provides tools for flu sequence analysis, annotation and submission to GenBank. It also provides links to other flu sequence resources, and publications and general information about flu viruses.

VecScreen

A system for quickly identifying segments of a nucleic acid sequence that may be of vector origin. VecScreen searches a query sequence for segments that match any sequence in a specialized non-redundant vector database (UniVec).

Downloads

BLAST (Stand-alone)

BLAST executables for local use are provided for Solaris, LINUX, Windows, and MacOSX systems. See the README file in the ftp directory for more information. Pre-formatted databases for BLAST nucleotide, protein, and translated searches also are available for downloading under the db subdirectory.

FTP: GenBank

This site contains files for all sequence records in GenBank in the default flat file format. The files are organized by GenBank division, and the full contents are described in the README.genbank file.

FTP: RefSeq

This site contains all nucleotide and protein sequence records in the Reference Sequence (RefSeq) collection. The "release" directory contains the most current release of the complete collection, while data for selected organisms (such as human, mouse and rat) are available in separate directories. Data are available in FASTA and flat file formats. See the README file for details.

FTP: UniVec

This site contains the UniVec and UniVec_Core databases in FASTA format. See the README.uv file for details.

Submissions

BankIt

A web-based sequence submission tool for one or a few submissions, designed to make the submission process quick and easy.

Barcode Submission

Tool to submit Barcodes, short nucleotide sequences from a standard genetic locus for use in species identification.

Sequin

A stand-alone software tool developed by the NCBI for submitting and updating entries to public sequence databases (GenBank, EMBL, or DDBJ). It is capable of handling simple submissions that contain a single short mRNA sequence, complex submissions containing long sequences, multiple annotations, segmented sets of DNA, as well as sequences from phylogenetic and population studies with alignments. For simple submission, use the online submission tool BankIt instead.

tbl2asn

A command-line program that automates the creation of sequence records for submission to GenBank using many of the same functions as Sequin. It is used primarily for submission of complete genomes and large batches of sequences.

Xinjiang discovery provides intriguing DNA link

CHANGCHUN, April 29 (Xinhua) -- The DNA of some 4,000 year-old bodies unearthed five years ago in Xinjiang, in northwest China, provides scientific evidence of early intermingling between people of European and Asian origin.

Zhou Hui, a professor of life science and her team discovered that some of the earliest inhabitants of the Tarim Basin in the Taklamakan Desert were of European and Siberian descent.

The basin, where hundreds of well-preserved mummies have been found since the 1980s, has attracted great attention from scientists worldwide.

Professor Victor Mair of Pennsylvania University claimed in 2006, "From around 1800 B.C. the earliest mummies in the Tarim Basin were exclusively Caucasoid, or Europoid," after he studied DNA samples derived from five bodies unearthed in the basin.

However, Professor Jin Li of Shanghai-based Fudan University, announced in 2007 that the mummies' DNA in the basin's Loulan area, including the 3,800-year-old Loulan Beauty, indicated East Asian, even South Asian origin.

Many archaeologists have accepted that people living in the basin as early as 3,800 years ago, or the Bronze Age, were of European descent, with Asians, mainly from east Asia, only arriving during the Iron Age, Zhou said. "But when the population from Europe and Asia began 'intermarrying' in the area still remains a mystery," she added.

Zhou and her team got DNA samples from the bones and teeth of 20 mummies, around 4,000-year-old. They were all excavated at the Xiaohe cemetery in the basin in 2004 and 2005.

The analyzed DNA profiles included the mitochondrial DNA, which is exclusively passed down through the mother, and the Y chromosome, passed down from father to son.

We found that DNA from five of the seven males derived from their mother, belonged to a lineage that came from Siberia, most likely from south or eastern Siberia, while their Y chromosome indicated European ancestry, Li Chunxiang, another researcher with the team, told Xinhua.

The seven males' Y chromosome had similarities to ancient Europeans who wandered the Eurasian Steppe, stretching roughly 3,000 miles from west to east, mainly in Central Asia.

People of the lineage can be found now in Eastern Europe, Central Asia and Siberia, but rarely in East Asia, Li said.

The mitochondrial DNA of five males and the nine other mummies (four females and five mummies whose gender is unknown) indicated they were related to an ancient lineage that can now be found mostly in modern Siberia, East Asia and Central Asia, Li said.

Their maternal lineage could be traced to Asian populations most likely lived in south Siberia, she said.

Two other females' DNA indicated their maternal ancestors had come from Western Europe.

"Our finding show the European and Siberian tribes began socializing with each other, even intermarrying, almost 4,000 years ago," Zhou said.

But scholars said the Europeans and Siberians might have met and intermarried outside the basin before their immigration into the basin.

"The civilization of the Tarim Basin, according to archaeological findings, arose very late. The 4,000-year-old mummies we found in Xiaohe are believed to be among the earliest inhabitants in the basin. But the Xiaohe people's DNA lineages are over 10,000 years old," Li said.

DNA with both European and Asian markings was also found in south Siberia. People of European origin had spread eastward into that region during the Bronze Age, she said.

The Xiaohe cemetery, 175 km west of the ancient city of Loulan, is located on the ancient Silk Road, once a booming trade route traversing the Asian continent.

The burial ground, with 167 graves, was first explored by Folke Bergman, a Swedish archaeologist in 1934. But it "vanished" until the Xinjiang Archaeological Institute rediscovered it in 2000, Zhou said.

The excavation of the cemetery began in 2002, but only experts with the institute and the Research Center for Chinese Frontier Archaeology of Jilin University were authorized to unearth the lowest layer where the oldest mummies were buried.

"We found 41 graves in this layer, and 37 of them had human remains. The corpses were lying in bottom-up-boat-like coffins. They all had distinctive European appearances and were well-preserved thanks to the dry air and good drainage." She said.

Some mummies unearthed in the Tarim Basin are displayed in a number of museums in Xinjiang, said Idelis Abdurisulu, former director with the Institute of Cultural and Historical Relics and Archaeology of Xinjiang Uygur Autonomous Region.

"The regional museum has six or seven mummies, while others are scattered around Xinjiang in some smaller museums," he said.

In late March, the Bowers Museum in Santa Ana in California began exhibiting two of the Tarim Basin mummies, including Xiaohe Beauty, a 3,800-year-old female, and Qiemo Baby, an infant aged eight to 10 months who died about 2,800 years ago.

Scientists hail 'revolutionary' kidney gene find

Chronic kidney disease causes the organs to function less effectivel

The identification of 20 genes which could help explain the causes of kidney disease could one day "revolutionise" treatment, researchers say.

Chronic kidney disease affects about one in 10 adults and can require dialysis or even an organ transplant.

The genes identified by the international team of researchers control kidney functions such as filtering waste from the blood.

Experts said the Nature Genetics study was "a great breakthrough".

Chronic kidney disease (CKD) is a long-term condition in which the kidneys progressively lose their function.

These are still early days but it is truly a great breakthrough Charles Kernahan, Kidney Research UK

People tend not to notice symptoms, which can include swollen ankles and hands or blood in the urine, until the condition is advanced.

It is linked to ageing - about one in five men and one in four women aged between 65 and 74 will have some degree of CKD.

The most common cause of CKD is damage caused by other long-term conditions, such as diabetes and high blood pressure.

It was known there was a genetic component to the disease, but not which genes were involved.

'First step'

In this study, an international team of scientists, including researchers at the University of Edinburgh, looked at the genes of nearly 70,000 people across Europe.

They found 13 new genes that influence renal function and seven others that affect the production and secretion of creatinine - a chemical waste molecule that is generated from muscle metabolism and filtered through the kidneys.

Dr Jim Wilson, a geneticist at the University of Edinburgh who worked on the study, said: "This work could revolutionise the treatment of kidney disease in the future - but this will take some time.

"It's a very critical first step towards a completely new understanding of the biology behind CKD. Transferring what we've found into clinical benefits will take some years."

Charles Kernahan, chief executive of the charity Kidney Research UK, said "These are still early days but it is truly a great breakthrough.

"No-one knows who will be affected or when kidney disease may strike next, so even more research needs to be funded to help us tackle this challenge."

(Source: BBC Science and Technology)

Autosomal dominant vs Autosomal recessive

Autosomal dominant

Main article: Autosomal dominant#Autosomal dominant gene

Only one mutated copy of the gene will be necessary for a person to be affected by an autosomal dominant disorder. Each affected person usually has one affected parent. There is a 50% chance that a child will inherit the mutated gene. Conditions that are autosomal dominant often have low penetrance, which means that although only one mutated copy is needed, a relatively small proportion of those who inherit that mutation go on to develop the disease. Examples of this type of disorder are Huntington's disease, Neurofibromatosis 1, Marfan Syndrome, Hereditary nonpolyposis colorectal cancer, and Hereditary multiple exostoses, which is a highly penetrant autosomal dominant disorder. Birth defects are also called congenital anomalies.

Autosomal recessive

Main article: Autosomal dominant#Autosomal recessive allele

Two copies of the gene must be mutated for a person to be affected by an autosomal recessive disorder. An affected person usually has unaffected parents who each carry a single copy of the mutated gene (and are referred to as carriers). Two unaffected people who each carry one copy of the mutated gene have a 25% chance with each pregnancy of having a child affected by the disorder. Examples of this type of disorder are cystic fibrosis, sickle-cell disease (also partial sickle-cell disease),Tay-Sachs disease, Niemann-Pick disease, spinal muscular atrophy, and Dry (otherwise known as "rice-brand") earwax.

Fossil Hunters and Their Amazing Achievements

9-Year-Old Fossil Hunter Finds 2-Million Old Human

9-Year-Old Fossil Hunter Finds 2-Million Old Human by Mitch Marconi A 9-year-old boy reportedly changed all though of evolution by finding a 2 million year old fossil. According to reports, Matthew Berger, found a fossilized collarbone of a child who ...

www.postchronicle.com/news/original/article_212295261.shtml ·

'Fossil hunter finds 140-million-year-old spider's web'…

http://www.telegraph.co.uk/science/science-news/6467024/Fossil-hunter-finds-140-million-year-old-spiders-web.html The tiny tangled filaments date back 140 million years and are linked to each other in the roughly circular pattern familiar to ...

richarddawkins.net/articles/4556 ·

Nine-Year-Old Fossil Hunter Finds New Species of Human…

Rescue Workers at Twin Towers Show Lung Problems 7 Years After 9/11 Attack ... The Cradle of Humankind, located 40 kilometers (25 miles) outside of Johannesburg, is also the place where the more than 2 million-year-old fossil of Australopithecus africanus

www.bloomberg.com/apps/news?pid=20601124&sid=aqFpdCaWxzl4

Man gets 60 days for dinosaur bones theft

... raptor fossil from a ranch in northern Montana. He is scheduled to be sentenced on July 9 in a separate federal case involving more fossils taken from Bureau of Land Management land. In 2000, Murphy discovered a mummified, 77-million-year-old ...

www.chinadaily.com.cn/world/2009-06/03/content_7973177.htm ·

FOSSIL HUNTER MARY LEAKEY DIES AT 83.(News ...

FOSSIL HUNTER MARY LEAKEY DIES AT 83.(News)(Obituary) ... find Seattle Post-Intelligencer articles. Mary Leakey, the world famous fossil hunter who in ... Mary Leakey and her husband, anthropologist Louis Leakey, who died in 1972 ...

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Fossil Hunter Presentations

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Nine-Year-Old Fossil Hunter Finds New Species of Human…

Nine-Year-Old Fossil Hunter Finds New Species of Human Ancestor Newsvine 2010-04-10 ... Is 2-million-year-old African fossil the missing link in human evolution? 2010-04-10 Newstrack India London, Apr 9 (ANI): Suggestions that the newly found ...

article.wn.com/view/2010/04/10/NineYearOld_Fossil_Hunter... ·

9-year-old Fossil Hunter Finds New Species of Human ...

A 9-year-old fossil hunter may have opened a new chapter in the evolutionary story of mankind when he found the fossilized collarbone of a child who lived almost - 9-year-old Fossil Hunter Finds ...

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Nine-Year-Old Fossil Hunter Finds New Species of Human…

Nine-Year-Old Fossil Hunter Finds New Species of Human Ancestor April 08, 2010, 10:15 AM EDT ... April 8 (Bloomberg) -- A 9-year-old boy who wandered from his father’s side may have opened a new chapter in the evolutionary story of mankind ...

www.businessweek.com/news/2010-04-08/nine-year-old-fossil...

50-million-year-old fossil horse unearthed

50-million-year-old fossil horse unearthed KEMMERER, Wyo. (AP)--Wyoming has lots of horses, wild horses, quarter horses and pack horses--all kinds of horses. ... As a fossil hunter for 30 years, Tynsky has also found a 13-foot crocodile some 20 ...

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9-year-old Fossil Hunter Finds New Species of Human ...

A 9-year-old fossil hunter may have opened a new chapter in the evolutionary story of mankind when he found the fossilized collarbone of a child who lived almost - 9-year-old Fossil Hunter Finds ...

celebglitz.com/38039/Celebrity-Gossip/9-year-old-fossil... ·

Nine-Year-Old Fossil Hunter Finds New Species of Human…

Nine-Year-Old Fossil Hunter Finds New Species of Human Ancestor April 08, 2010, 10:15 AM EDT ... April 8 (Bloomberg) -- A 9-year-old boy who wandered from his father’s side may have opened a new chapter in the evolutionary story of mankind ...

www.businessweek.com/news/2010-04-08/nine-year-old-fossil... ·

50-million-year-old fossil horse unearthed

50-million-year-old fossil horse unearthed KEMMERER, Wyo. (AP)--Wyoming has lots of horses, wild horses, quarter horses and pack horses--all kinds of horses. ... As a fossil hunter for 30 years, Tynsky has also found a 13-foot crocodile some 20 ...

www.hpj.com/.../2004/jun04/jun14/50-million-year-oldfossilho.CFM ·

D.C.'s Youngest Fossil Hunter | NBC Washington ...

But a local 9-year old girl, Gabrielle Block, is having the last laugh. She snatched up a 100-million-year-old tailbone out of the Dino Park last week, reports the Post. ... http://www.nbcwashington.com/news/local-beat/DCs-Youngest-Fossil-Hunter .

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·

9-Year-Old Finds Dinosaur Fossil | Geology.com

9-Year-Old Finds Dinosaur Fossil November 28, 2009 | MyFoxDC.com A 9-year-old girl from Annandale, Maryland found a fragment of a dinosaur vertebrae at a newly-opened dinosaur park where visitors can help paleontologists. ... Fossil ...

geology.com/news/2009/9-year-old-finds-dinosaur-fossil.shtml ·

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The child of a poor family, Mary became a fossil hunter, inspiring the tongue-twister, “She Sells Sea Shells by the Seashore.” ... From Palgrave Macmillan Pub date: Oct 2009 256 pages Size 6-1/8" x 9-1/4" $27.00 - Hardcover (0-230-61156-7) ...

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FARK.com: (2317360) 100-million-year-old fossil of ...

100-million-year-old fossil of stingray fails to sell at auction; provides media with opportunity to remind us that Steve Irwin is still dead ( ... How can the fossil be 100 million years old when the earth itsself is less the 100 thousand years old??? ...

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Soft tissue taken from 68 million-year-old…

Soft tissue taken from 68 million-year-old Tyrannosaurus rex fossil yields original protein ... 10 hours ago | 5 / 5 (9) | 2 | (PhysOrg.com) -- Scientists funded by the Biotechnology and Biological Sciences Research Council (BBSRC) at ... The hunter ...

www.physorg.com/news95606831.html ·

47M-Year-Old Fossil Evolutionary 'Aunt' to Humans

Mar 31, 10 9:12 PM CDT ... Scientists have discovered the oldest intact primate fossil on record, ABC News reports. Nicknamed “Ida,” the 47-million-year-old lemur-like creature had opposable thumbs, fingernails instead of claws, and ...

www.newser.com/story/59501/47m-year-old-fossil-evolutionary... ·

What information about a genetic condition can statistics provide?

Statistical data can provide general information about how common a condition is, how many people have the condition, or how likely it is that a person will develop the condition. Statistics are not personalized, however—they offer estimates based on groups of people. By taking into account a person’s family history, medical history, and other factors, a genetics professional can help interpret what statistics mean for a particular patient.

Some statistical terms are commonly used when describing genetic conditions and other disorders. These terms include:

Common statistical terms
Statistical term	Description	Examples
Incidence	The incidence of a gene mutation or a genetic disorder is the number of people who are born with the mutation or disorder in a specified group per year. Incidence is often written in the form “1 in [a number]” or as a total number of live births.	About 1 in 200,000 people in the United States are born with syndrome A each year. An estimated 15,000 infants with syndrome B were born last year worldwide.
Prevalence	The prevalence of a gene mutation or a genetic disorder is the total number of people in a specified group at a given time who have the mutation or disorder. This term includes both newly diagnosed and pre-existing cases in people of any age. Prevalence is often written in the form “1 in [a number]” or as a total number of people who have a condition.	Approximately 1 in 100,000 people in the United States have syndrome A at the present time. About 100,000 children worldwide currently have syndrome B.
Mortality	Mortality is the number of deaths from a particular disorder occurring in a specified group per year. Mortality is usually expressed as a total number of deaths.	An estimated 12,000 people worldwide died from syndrome C in 2002.
Lifetime risk	Lifetime risk is the average risk of developing a particular disorder at some point during a lifetime. Lifetime risk is often written as a percentage or as “1 in [a number].” It is important to remember that the risk per year or per decade is much lower than the lifetime risk. In addition, other factors may increase or decrease a person’s risk as compared with the average.	Approximately 1 percent of people in the United States develop disorder D during their lifetimes. The lifetime risk of developing disorder D is 1 in 100.

How are genetic conditions and genes named?

Naming genetic conditions

Genetic conditions are not named in one standard way (unlike genes, which are given an official name and symbol by a formal committee). Doctors who treat families with a particular disorder are often the first to propose a name for the condition. Expert working groups may later revise the name to improve its usefulness. Naming is important because it allows accurate and effective communication about particular conditions, which will ultimately help researchers find new approaches to treatment.

Disorder names are often derived from one or a combination of sources:
The basic genetic or biochemical defect that causes the condition (for example, alpha-1 antitrypsin deficiency);

One or more major signs or symptoms of the disorder (for example, sickle cell anemia);

The parts of the body affected by the condition (for example, retinoblastoma);
The name of a physician or researcher, often the first person to describe the disorder (for example, Marfan syndrome, which was named after Dr. Antoine Bernard-Jean Marfan);

A geographic area (for example, familial Mediterranean fever, which occurs mainly in populations bordering the Mediterranean Sea); or

The name of a patient or family with the condition (for example, amyotrophic lateral sclerosis, which is also called Lou Gehrig disease after a famous baseball player who had the condition).

Disorders named after a specific person or place are called eponyms. There is debate as to whether the possessive form (e.g., Alzheimer’s disease) or the nonpossessive form (Alzheimer disease) of eponyms is preferred. As a rule, medical geneticists use the nonpossessive form, and this form may become the standard for doctors in all fields of medicine.

Naming genes

The HUGO Gene Nomenclature Committee (HGNC) designates an official name and symbol (an abbreviation of the name) for each known human gene. Some official gene names include additional information in parentheses, such as related genetic conditions, subtypes of a condition, or inheritance pattern. The HGNC is a non-profit organization funded by the U.K. Medical Research Council and the U.S. National Institutes of Health. The Committee has named more than 13,000 of the estimated 20,000 to 25,000 genes in the human genome.

During the research process, genes often acquire several alternate names and symbols. Different researchers investigating the same gene may each give the gene a different name, which can cause confusion. The HGNC assigns a unique name and symbol to each human gene, which allows effective organization of genes in large databanks, aiding the advancement of research. For specific information about how genes are named, refer to the HGNC’s Guidelines for Human Gene Nomenclature .