454

I have been trying to understand the pyrosequencing technology, popularly known as 454. The very first question which came to my mind is WHY it is called 454? Is it because .454 kasool Handgun is sleeker then Shotgun ( Cf. Whole Genome Shotgun Sequence ) and slowly becoming as powerful ... or is it because of the fact that "In one instrument run sequence a minimum of 20 million base pairs in 4.5 hours" ... just a conjecture, if you guys have a proof, please share !
Anyways coming back to the technology, what I understand (below is a crude attempt to visualize it) is that there are 4 containers containing A,T,G and C which sequentially pass over the bowl containing a mixture of Polymerase, Sulfurylase, Luciferase, Apyrase and the DNA fragment to be sequenced. The addition of the nucleotide will light up ( thanks to lucifer-ase ) the CCD (a thing close to what we have in a digital camera and the costliest part of the instrument). Since we know the culprit nucleotide container, peak telling how many of that nucleotide is added, we can sequentially proceed and keep adding letters to the reads... this is happening in a massively parallel fashion and that brings out the power of 454...

Biocomputing

Haynes et al. in the article "Engineering bacteria to solve the Burnt Pancake Problem" [ http://www.jbioleng.org/content/2/1/8#IDAJQH0E ] demonstrate how one can take advantage of direction sense embedded in DNA by coding 5'-3' as 0 and 3'-5' as 1 binary coding to convert cells into computers.

clipped from www.msnbc.msn.com Ron Weiss, an assistant professor of electrical engineering and molecular biology at Princeton University, said the new study provides a “nice demonstration that there’s some capability to instruct cells to carry out computational tasks. And I think this certainly brings a new aspect to what’s been demonstrated before.” Weiss, who wasn’t involved with the research, said the effort is another sign that the field is progressing, despite its relative infancy. “We really are at the beginning, at the vacuum tube stage or something like that, if you use the comparison with computer electronics,” he said.

International Conference on Functional Programming 2008

The 11th ICFP ( http://icfpcontest.org/ ) Programming Contest is from Friday, July 11, 2008 to Monday, July 14, 2008. More details on what the contest is like, check out http://cpoucet.wordpress.com/2008/06/11/icfp-contest-2008/ .
Mail queries to Tim Sheard at sheard@cs.pdx.edu.

clipped from lambda-the-ultimate.org The ICFP Programming Contest is one of the most advanced and prestigious programming contests, as well as being a chance to show off your programming skills, your favorite languages and tools, and your ability to work as a team. The contest is affiliated with the International Conference on Functional Programming. Teams consisting of one or more participants, from any part of the world, using any programming language, may enter.

Unofficial Google Shell

I have been waiting for google shell. I thought they will name it gshell, but it turns out:
goosh.org - the unofficial google shell ( http://goosh.org/ ).
It is pretty neat and useful in its neonatal state itself, like to read a feed, you can type, for eg:

r http://www.google.com/reader/public/atom/user/11136726768885096694/label/cbn-roll

and gets default 4 latest feeds, or you can check out a ncbi accession by typing, for eg:

NP_001108376

and get to the Fugu fish refseq link.

The most useful thing is the fact that it it text based and quite easy to parse visually as well as via scripts.
Another cool feature for me right now is the shell translation, like to get the english word for the norwegian word 'hvor', all I have to do is type:

t no en hvor

which correctly says:
translating "hvor" from "no" to "en":

"where"

More discussion going on at http://tech.slashdot.org/article.pl?sid=08/06/02/222234&from=rss .
Enjoy!

clipped from goosh.org Goosh goosh.org 0.4.3-beta #1 Mon, 02 Jun 08 22:28:01 UTC Google/Ajax help command aliases parameters function web (search,s,w) [keywords] google web search lucky (l) [keywords] go directly to first result images (image,i) [keywords] google image search wiki (wikipedia) [keywords] wikipedia search clear (c) clear the screen help (man,h,?) [command] displays help text news (n) [keywords] google news search blogs (blog,b) [keywords] google blog search feeds (feed,f) [keywords] google feed search open (o) <url> open url in new window go (g) <url> open url more (m) get more results in (site) <url> <keywords> search in a specific website load <extension_url> load an extension video (videos,v) [keywords] google video search read (rss,r) <url> read feed of url place (places,map,p) [address] google maps search lang <language> change language addengine add goosh to firefox search box translate (trans,t) [lang1] [lang2] <words> google translation

Conserved Domain Database (CDD) has been updated

The CDD [ http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml ] and the its search tool [ http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi ] has been recently updated. Also check out the latest approach for "automatically assigning subcellular locations" to protein from Newberg and Murphy [ http://pubs.acs.org/cgi-bin/abstract.cgi/jprobs/asap/abs/pr7007626.html ], more at http://www.sciencedaily.com/releases/2008/05/080512145232.htm .

clipped from beckerinfo.net

CQNCer , players in dna sequencing

So finally we see Helicos in action (via http://microarray.wordpress.com/2008/04/11/entire-genome-sequencing-from-single-molecule-dna/ ) , http://www.sciencemag.org/cgi/content/full/320/5872/106 .
They have sequenced the M13 phage virus (about .3 mill bases) ... sometime back I was surveying the trends in sequencing and captured them at http://www.slideshare.net/sharma_animesh/cqncer .
These strategies are generally being used for reqsequencing or sequencing smaller genomes. Though I see that even smaller genomes like Stenotrophomonas maltophilia ( Steno, http://genomebiology.com/2008/9/4/R74 ) done the old way... more at http://www.biologynews.net/archives/2008/05/07/superbug_genome_sequenced.html . Same goes for recently sequenced Platypus gnome ( http://www.nature.com/nature/journal/v453/n7192/abs/nature06936.html , http://www.eurekalert.org/pub_releases/2008-05/embl-pgs050608.php ) and the Papaya genome draft ( http://www.nature.com/nature/journal/v452/n7190/abs/nature06856.html , http://www.biologynews.net/archives/2008/05/14/scientists_decipher_fruit_tree_genome_for_the_first_time.html ) but given these new cheaper sequencing technologies and better algorithms, we are bound to see cooler changes in Tree-of-Life ( http://www.boston.com/news/science/articles/2008/04/28/tree_of_life_continues_to_evolve/ ) !

clipped from www.ncbi.nlm.nih.gov The Genome database provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps. The database is organized in six major organism groups: Archaea, Bacteria, Eukaryotae, Viruses, Viroids, and Plasmids and includes complete chromosomes, organelles and plasmids as well as draft genome assemblies.