List of Amino Acids

1. alanine - ala - A
2. arginine - arg - R
3. asparagine - asn - N
4. aspartic acid - asp - D
5. cysteine - cys - C
6. glutamine - gln - Q
7. glutamic acid - glu - E
8. glycine - gly - G
9. histidine - his - H
10. isoleucine - ile - I
11. leucine - leu - L
12. lysine - lys - K
13. methionine - met - M
14. phenylalanine - phe - F
15. proline - pro - P
16. serine - ser - S
17. threonine - thr - T
18. tryptophan - trp - W
19. tyrosine - tyr - Y
20. valine - val - V

There are some new amino acids discovered after them, they are

21. selenocysteine

22. pyrrolysine

Red Hat tries spreading open-source idea

source: cnet news

Red Hat is taking a second crack at trying to spread its open-source philosophy beyond the realm of software development.

On Wednesday, the Raleigh, N.C.-based Linux seller announced a partnership with the nearby University of North Carolina to try to encourage use of the open, collaborative model in the fields of health care research, biotechnology, bioinformatics and public policy.

"The history of open source has taught us that the more broadly and transparently information is shared and re-used, the faster and stronger the results," Joanne Rohde, Red Hat's executive vice president of operations, said in a statement.

The move hearkens back to 1999, when the company launched the Red Hat Center for Open Source, with company co-founder Marc Ewing leading the effort. In an interview at the time, Ewing said, "What we want to be able to do is facilitate thinking and discussion about the principles of open source and how they apply in communities other than the software development community--law, medicine, business, governance, scientific research, education."

That earlier effort fizzled. This time, however, the company has a partner.

"We need to know what works faster, better and cheaper than we could do in the past. That means collecting data from more sources, not just in teaching hospitals...but in all settings where new technologies are being used--private practices, health departments, health education centers and walk-in clinics," said Etta Pisano, vice dean for academic affairs at the University of North Carolina's Biomedical Research Imaging Center.

Superbugs-Interesting one!!

Stainless steel door handles and taps at a hospital are being replaced with copper ones in an effort to reduce the presence of superbugs Staphylococcus aureus MRSA and Clostridium difficile.Birmingham's Selly Oak Hospital is swapping steel for copper in an 18-month trial to test the findings. 80% of hospital MRSA transmission is believed to come from contact with surfaces such as door handles, bathroom taps, toilet flush handles and grab rails. To test the theory one general medical ward is having copper installed in preparation for the trial while a similar ward will retain its traditional fittings. Even pens used by staff will be made from copper alloy. Copper reacts with the bacteria and inhibits respiration - the Egyptians may have used copper thousands of years ago to treat infections.

So wat are superbugs?

If a bacterium carries several resistance genes, it is called multiresistant or, informally, a superbug.

Bioinformatics Grad schools!!

hi blog readers,

i've jus made up a summary of all bioinformatics schools in UG/PG category.. May b i'll start posting n a couple of days.. Plz await for them.. If u've any queries, jus comment i'll respond 2 u..

U can also review some universities, colleges, certificate programs n send it 2 bioinfinite@hotmail.com... Any contributions u wanna do to bioinfinite (may be some articles, descriptors of any topics, link,etc..) , send n urs to above mail_id.. Keep urself updated..

Phenomics

Phenomics describes the state of an organism as it changes with time. It is a word he coined at a guest lecture he gave at the University of Waterloo in 1996 by Steven A. Garan, Director of the Aging Research Centre (ARC).

Then what s meant by phenome??

Answer is right down..

A phenome is the set of all phenotypes expressed by a cell, tissue, organ, organism, or species. A phenome includes phenotypic traits due to either genetic or environmental influences.

Just as the genome and proteome signify all of an organism's genes and proteins, the phenome represents the sum total of its phenotypic traits. Some examples of human phenotypes are skin color, eye color, height, or specific personality characteristics. Phenotypic differences between individuals can be due to environmental influences, genetic variation such as single nucleotide polymorphisms (SNPs), or a combination of the two.

Phenomics is the study of the nature of phenotypes and how they are determined, particularly when studied in relation to the set of all genes (genomics) or all proteins (proteomics).

SMD : Stanford Microarray Database

SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. SMD provides interfaces for data retrieval, analysis and visualization.

SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization.

Link: http://genome-www5.stanford.edu/

Junk DNA

"Junk" DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. About 97% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA. While much of this sequence may be an evolutionary artifact that serves no present-day purpose, some is believed to function in ways that are not currently understood.

Moreover, the conservation of some junk DNA over many millions of years of evolution may imply an essential function.

8% of human junk DNA has been shown to be formed by retrotransposons of Human Endogenous Retroviruses (HERVs).

Junk DNA may act as a protective buffer against genetic damage and harmful mutations.Junk DNA may have no function.

For example, recent experiments removed 1% of the mouse genome and were unable to detect any effect on the phenotype. This result suggests that the DNA is, in fact, non-functional.

Research Nuggets:
A 2006 study by the McKusick-Nathans Institute of Genetic Medicine (Johns Hopkins) stated that "Junk DNA may not be so junky after all."
Researchers at the University of Illinois Society for Experimental Biology found an antifreeze-protein gene in a species of fish which "evolved" from junk DNA.
A mathematical analysis of the genetic code by IBM identified patterns that suggested junk DNA had an important role after all.
In 2006, University of Iowa researchers documented segments of RNA (previously considered "junk") that regulated protein production, and could generate microRNAs.

BLAST Beta

NCBI is holding a beta test for a new BLAST interface design.

One major improvement is a new "Recent Results" feature that provideslinks to all of your recent BLAST search results.

Another is "SavedStrategies", which allows you to save BLAST forms with their parameters and use them later. Saved Strategies requires a free MyNCBI account, andis compatible with existing accounts. Signing in to MyNCBI also makesyour Recent Results available from any browser.

Other improvements include:-

-Easier navigation

- Simplified BLAST program selection

- Easy access to genome searches

- Improved Organism selection with species name auto-complete

- Automatic parameter adjustment to optimize for short queries

- A user-specifiable title for each BLAST job

The Beta test is available HERE

Folding @ Home - Distributed Computing

To my reviewer's request, i've posted this,

Folding @ Home is an initiative started by Stanford University to have a distributed computing environment, where each online user can contibute a share of his/her computer process to the folding program( we've to download the program and install it to be a part of the Project). Folding@Home uses novel computational methods coupled to distributed computing, to simulate problems thousands to millions of times more challenging than previously achieved.

Since October 1, 2000, over 1,000,000 CPUs throughout the world have participated in Folding@Home. Each additional CPU gives them an added boost in performance, allowing them to tackle more difficult problems or solve existing research faster or more accurately.

you can access this at http://folding.stanford.edu/

One more project is also available, named Genome@Home (Pande Lab) at http://genomeathome.stanford.edu

Mathematician Probes Geometric Route To Combat Viruses

source: Science Daily

A mathematician at the University of York has been awarded a Research Leadership Award of more than £700,000 by the Leverhulme Trust to study the geometry of viruses.

Viruses have highly symmetrical external shells formed from proteins that encapsulate the viral genome. Dr Twarock has developed a method for encoding the structures of these protein shells that pinpoint the locations of the proteins and the bonds between them. With collaborators Professor Cristian Micheletti, from the International School for Advanced Studies (SISSA) in Trieste, Italy, and Professor Anne Taormina, from the University of Durham, she has used these results to model the assembly of viruses.

Subsequent work with collaborators Professor Peter Stockley, Dr Neil Ranson and their groups at the Astbury Centre for Structural Molecular Biology at the University of Leeds suggests that not only the geometry of the viral capsids themselves but also the full three-dimensional structures of the particles are constrained. The implications of this discovery on virus assembly are currently being investigated.

Database of incorrect Protein conformations

Decoys ‘R’Us database contains a wide variety of decoys generated by different methods with the aim of fooling scoring functions.

Decoys are computergenerated conformations of protein sequences that possess some characteristics of native proteins, but are not biologically real.

Decoys have been based on discrete-state models, molecular dynamics trajectories, crystal structures of different resolutions ,conformations with different loops, and amino acid sequences mounted on radically different folds.In other words, this database provide incorrect conformations data in order to improve the protein structure prediciton.

Organisation of decoy sets

1.The multiple decoy sets

2.The single decoy sets

3.The loop decoy sets

The current version of the entire decoy set is only available as a single tar and gzipped file to download.

Link: Decoys 'R' Us database

Human Protein Reference Database

Human Protein Reference Database (HPRD) that integrates information relevant to the function of human proteins in health and disease.Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization for each protein in the human proteome.

Go to Human Protein Reference Database