Bioinformatics Database



1.Nucleotide Sequence Databases
1.1 International Nucleotide Sequence Database Collaboration
Database name
Full name and/or description
URL
DDBJ-DNA Data Bank of Japan
All known nucleotide and protein sequences
EMBL-Nucleotide Sequence Database
All known nucleotide and protein sequences
GenBank
All known nucleotide and protein sequences


1.2. DNA sequences: genes, motifs and regulatory sites



1.2.1. Coding and coding DNA


Database name
Full name and/or description
URL
ACLAME
A classification of genetic mobile elements
CUTG
Codon usage tabulated from GenBank
Genetic Codes
Genetic codes in various organisms and organelles
Entrez Gene
Gene-centered information at NCBI
HERVd
Human endogenous retrovirus database
Hoppsigen
Human and mouse homologous processed pseudogenes
Imprinted Gene Catalogue
Imprinted genes and parent-of-origin effects in animals
Islander
Pathogenicity islands and prophages in bacterial genomes
MICdb
Prokaryotic microsatellites
NPRD
Nucleosome positioning region database
STRBase
Short tandem DNA repeats database
TIGR Gene Indices
Organism-specific databases of EST and gene sequences
Transterm
Codon usage, start and stop signals
UniGene
Non-redundant set of eukaryotic gene-oriented clusters
UniVec
Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination
VectorDB
Characterization and classification of nucleic acid vectors
Xpro
Eukaryotic protein-encoding DNA sequences, both intron-containing and intron- less genes

1.2.2. Gene structure, introns and exons, splice sites


Database name
Full name and/or description
URL
ASAP
Alternative spliced isoforms
ASD
Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb
ASDB
Alternative splicing database: protein products and expression patterns of alternatively spliced genes
ASHESdb
Alternatively spliced human genes by exon skipping database
EASED
Extended alternatively spliced EST database
ECgene
Genome annotation for alternative splicing
EDAS
EST-derived alternative splicing database
ExInt
Exon intron structure of eukaryotic genes
HS3D
Homo sapiens splice sites dataset
Intronerator
Alternative splicing in C.elegans and C.briggsae
SpliceDB
Canonical and non-canonical mammalian splice sites
SpliceInfo
Modes of alternative splicing in human genome
SpliceNest
A tool for visualizing splicing of genes from EST data

1.2.3. Transcriptional regulator sites and transcription factors

Wednesday, August 24, 2011 Tags: , , 0 comments

Beginning ASP.NET 2.0 with C#

Tuesday, January 4, 2011 Tags: , 0 comments

Bioremediation: Principles and Applications By Ronald L. Crawford, Don L. Crawford, PDF


Ronald L. Crawford, Don L. Crawford, quot;Bioremediation: Principles and Applicationsquot;
Cambridge University Press | 1997 | ISBN: 0521470412, 052101915X | 412 pages | File type: PDF | 10,4 mb
Industrial and agricultural activity throughout this century has led to considerable contamination of soil and groundwater resources by hazardous chemicals. The technique of bioremediation uses living organismsusually bacteria and fungito remove pollutants from soil and water with minimal disturbance to these environments. This approach, which is potentially more cost-effective than traditional techniques such as incineration of soils and carbon filtration of water, requires an understanding of how organisms transform chemicals, how they survive in polluted environments, and how they can be used in the field. This book examines these issues for many of the most serious and common environmental contaminants, presenting the most recent position on the application of bioremediation to polluted soil and water.



? Comprehensive - all important classes of organic pollutant covered in a single volume ? Practical emphasis - illustrates how to clean up various pollutants by biological means ? Authoritative - contributions from all the leading experts in this area combine to make a unique, multidisciplinary information resource ? For academics in microbiology and environmental science, also industrial and government scientists in pollution control
Contents

Preface D. Crawford; 1. Introduction R. Crawford; 2. Engineering of bioremediation processes W. Admassu and R. A. Korus; 3. Bioremediation in soil: influence of soil properties on organic contaminants and bacteria M. J. Morra; 4. Biodegradation of 'BTEX' hydrocarbons under anaerobic conditions L. Crumholtz, M. E. Caldwell and J. M. Suflita; 5. Bioremediation of petroleum contamination E. Rosenberg and E. Zon; 6. Bioremediation of environments contaminated by polycyclic aromatic hydrocarbons J. Mueller, C. Cerniglia and P. Pritchard; 7. Bioremediation of nitroaromatic compounds S. B. Funk, D. Crawford and R. Crawford; 8. A history of PCB biodegradation R. Unterman; 9. Bioremediation of chlorinated phenols J. Puhakka and E. Melin; 10. Biodegradation of chlorinated aliphatic compounds L. Wackett; 11. Microbial remediation of metals T. Roane, I. Pepper, R. Miller; 12. Molecular techniques in bioremediation M. Shields and S. Francesconi; Index.
Review

The editors of this book and the contributing authors should be congratulated in providing an up to date review of this rapidly developing subject and it should be of use to many scientists interested in Bioremediation. The Association of Applied Biologists News
Download
http://uploading.com/files/am114998/0521470412Bioremediation.rar/



http://www.megaupload.com/?d=1509IFA3

Thursday, October 28, 2010 Tags: , 0 comments

Photovoltaics 'Self-repairing' Solar Cell

Self-renewing solar cells grow like plants
Scientists at MIT mimic plant processes to build solar cells that renew themselves like living beings.
Living things don't have that many advantages over machines. We're not as quick, or as precise, and we don't have as good a memory. Moreover, while they are made of tough stuff, we are mostly composed of things that go squish. One of the limited advantages we have is that when we go squish, we have built-in repair shops. When they go crunch, they're crunched.
Self-renewal has been a goal of many different technology manufacturers, but especially the makers of solar cells. For years scientists have looked resentfully at their solar cells, the components of which wear out or break, and envied plants, which have a built-in systems that take apart and renew any worn-out bits.
MIT researchers have found a way to imitate this process:

Thursday, October 7, 2010 Tags: , 0 comments

Structure and Function in Cell Signalling.PDF

Structure and Function in Cell Signalling E Book

John Nelson
Pub: Wiley Blackwell

Size :10 MB
Page:411


Sequence analysis

Sequence analysis is the application of Information Technologies to Molecular Biology. It deals with biological sequences, and processes them to extract significant information that may yield new insights and guidelines in the understanding of biological organisms
Basics for sequence analysis

Proteins

A protein is typically built of a series of basic blocks called amino acids , chained together in a linear sequence of blocks. Amino acids may come in a variety of shapes and properties: they may be small or bulky, hidrophobic or hidrophyllic, electrically charged or neutral, etc... hence allowing for very complex shapes and interactions to be produced.

Amino acids are commonly referred to by name or by an abbreviation, usually in three or one letter. This allows for more efficient descriptions of how they are chained together to build a protein:
Neutral-Nonpolar
3-letter
1-letter
Glycine
Gly
G
L-Alanine
Ala
A
L-Valine
Val
V
L-Isoleucine
Ile
I
L-Leucine
Leu
L
L-Phenylalanine
Phe
F
L-Proline
Pro
P
L-Methionine
Met
M
Neutral-Polar
 
 
L-Serine
Ser
S
L-Threonine
Thr
T
L-Tyrosine
Tyr
Y
L-Tryptophan
Trp
W
L-Asparagine
Asn
N
L-Glutamine
Gln
Q
L-Cysteine
Cys
C
Acidic
 
 
L-Aspartic
Asp
D
L-Glutamic
Glu
E
Basic
 
 
L-Lysine
Lys
K
L-Arginine
Arg
R
L-Histidine
His
H

What is Bioinformatics..?

Bioinformatics derives knowledge from computer analysis of biological data. These can consist of the information stored in the genetic code, but also experimental results from various sources, patient statistics, and scientific literature. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics is a rapidly developing branch of biology and is highly interdisciplinary, using techniques and concepts from informatics, statistics, mathematics, chemistry, biochemistry, physics, and linguistics. It  has many practical applications in different areas of biology and medicine.
Roughly, bioinformatics describes any use of computers to handle biological information. In practice the definition used by most people is narrower; bioinformatics to them is a synonym for "computational molecular biology"- the use of computers to characterize the molecular components of living things.
Definition of Bioinformatics form various sources:-
  • Bioinformatics is the science of developing computer databases and algorithms for the purpose of speeding up and enhancing biological research. (source: www.whatis.com)
  • As a discipline that builds upon computational biology, bioinformatics encompasses the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. 

DNA Computers A Tech Of Tomorrow

Engineers have long dreamed of using DNA as the backbone for the next generation of computer circuits. New research shows just how it might be done.
Instead of conventional circuits built of silicon that use electrical current, computer engineers could take advantage of the unique properties of DNA, the double-helix molecule that carries life’s information.
“Conventional technology has reached its physical limits," said Chris Dwyer, assistant professor of electrical and computer engineering at Duke University's Pratt School of Engineering.
Dwyer recently demonstrated that by simply mixing customized snippets of DNA and other molecules, he could create billions of identical, tiny, waffle-looking structures.
These nanostructures can then be used as the building blocks for a variety of circuit-based applications, ranging from the biomedical to the computational.
Key to the promise of these DNA nanostructures is an ability to rapidly "switch" between zeros or ones -- the basic on/off binary action that powers computation. Light can be used to stimulate similar binary responses from DNA-based switches, though at a much faster rate than in silicon.
“When light is shined on the chromophores" -- parts of DNA responsible for its color -- "they absorb it, exciting the electrons,” Dwyer said. “The energy released passes to a different type of chromophore nearby that absorbs the energy and then emits light of a different wavelength. That difference means this output light can be easily differentiated from the input light, using a detector.”
Dwyer added: "This is the first demonstration of such an active and rapid processing and sensing capacity at the molecular level."
Building computers with life's building blocks

Friday, February 26, 2010 Tags: , 0 comments

Launching A New Biotechnology Magazine

Now We Are going to launch a biotechnology magazine Which will surely help you guy's to go through new technology's and inventions of biotechnology.

Wednesday, February 3, 2010 Tags: , , 0 comments

GMO Tomatoes Could Stay Fresh For Over a Month



sustainable design, green design, sustainable food, gmo, 
genetically modified organisms, tomatoes, plants, pesticides, green 
design
Many of us invested in the success of sustainable agriculture have a knee-jerk response against genetically-modified foods, and for good reason — they often come with patent protection, pesticides, and other undesirable features. But a new development from the National Institute of Plant Genome Research in New Delhi suggests that GMO crops could have at least one positive use: dramatically increasing the shelf life of fruits and vegetables.
sustainable design, green design, sustainable food, gmo, 
genetically modified organisms, tomatoes, plants, pesticides, green 
design 
Photo by The Ewan

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