Page 2 of 8 Great new genetic self-decoding bio-machine photos!    Latest pictures in the gene self decoding bio-machine How bout some beautiful gal pics!    Havn't i helped you with this info? Please do make a donation below via Paypal Whatever Genome Yip-Yap Hype you heard, now the job really starts! Fantastic new discoveries of the Gene Machine ( 3D   Pic's available as well! )  Genetic Composition Jul/Aug 2000: Genomic research was easy. Now the job really starts! Atlas of Protein Visualization and Side-Chain Interactions Reverse engineering code If you have a Genomic or biotech product, service available or program you would like to advertise with us, or us to advertise for you, please make contact here @: please submit e-mail request here: Please be specific! OR Visit our general affiliate info site at: submit-it affiliate programs ------------------------------- DAVID Frequently Asked Questions DAVID: ( Database for Annotation, Visualization, and Integrated Discovery ) 1. What is DAVID? 2. How do I analyze my gene lists? 3. What accession numbers and gene identifiers does DAVID accept? 4. What file formats can be uploaded/downloaded by DAVID? 5. How do I paste a list of gene identifiers? 6. Where does DAVID's annotation come from and how current is it?  7. Who do I contact if I find an annotation error? 8. How are genes counted in the GoCharts, KeggCharts, and DomainCharts tools? 9. Why are there different levels for GoCharts? 10. What does unclassified mean? 11. How do I cite DAVID? 12. What is the purpose of the minimum number of hits threshold? 13. What is really going on behind the scenes when I chose lets say level 1 compared to Level 5.  What else is being done in Level 5 that is not in Level 1? 14. Is the Domain Charts most beneficial for categorizing ESTs?  How else can I take advantage of this module? 15. What journal articles have made use of DAVID or EASE? 16. Not all of my genes are annotated!  Why?  Domai girl of Today -------------------------------------------------------------------- yahoo search for: spirm cell #1 0f 8 ( about 352,000 exist with correct spelling "sperm" ) 1.) CELL STRUCTURE ... meiosis. meiosis is cell division of a mothers egg after being fertilized by a spirm. ---- some DNA facts. ... www.vif.com/users/chris-m/medical/cell-structure.html ----------------------------------------------------- google search for: unfolding protein interactive Results 1 - 10 of about 2,670 7.) Genetic Composition | Unfolding and viewing the Protein ... can be characterized, visualization is the obvious tool for understanding protein but proteins cannot ... Disney's Atlantis Disney Interactive Norton Internet ... www.vif.com/users/chris-m/medical/genome2.html For more info on protein folding, folding errors, cell copying and division please visit: human-inbreeding Attempting to put molecular structure together: After the discoveries of Watson and Crick, the question that remained was how the DNA directs the formation of proteins, compounds central to all the processes of life. Proteins are the major components of most cell structures, and they control virtually all the chemical reactions that occur in living matter. The ability of a protein to act as part of a structure, or as an enzyme affecting the rate of a particular chemical reaction, depends on its molecular shape (see Molecule). This shape, in turn, depends on its composition. Every protein is made up of one or more components called polypeptides, and each polypeptide is a chain of sub-units called amino acids. Twenty different amino acids are commonly found in polypeptides. The number, type, and order of amino acids in a chain ultimately determine the structure and function of the protein of which the chain is a part. ----------------------------------------------------------------- google Searched the web for: BSE Statistics. Results 11 - 20 of about 94,200. 17.) BSE and more baffling genetic research statistics and the future ... ... Recherche Google: bse statistics google search for: bse+statistics we're #34 of 1,500 with the this web site! www.vif.com/users/chris-m/medical/genome8.html. ... www.vif.com/users/chris-m/medical/genome8.html ------------------------------------------ messanger+DNA MSN Preview results our VIF site Entry Page: cell-structure.html --------------------------------- yahoo.ca search for: Basic About RNA 8.) DNA-RNA MAKEUP TOP 20 WEB RESULTS out of about 5,820 ... DNA-RNA: Legal Internet Guide Legal Internet Guide. Basic DNA and RNA Protocols. Basic DNA and RNA Protocols 08960333:Product Link on Barnes & Noble.com. ... www.vif.com/users/chris-m/medical/dna-rna.html ----------------------------------------------------------------- google searched the web for dna + pictures. Results 31 - 40 of about 381,000 3.) DNA-RNA MAKEUP ... Frontiers in Molecular Biology Gene Families: Studies of DNA, RNA, Enzymes and Proteins 02) 04:26 AM google.com 12-225-75-239.client.attbi.com rna dna pictures. ... www.vif.com/users/chris-m/medical/dna-rna.html --------------------------------------------- google searched the web for: protein folding pictures. results 21 - 30 of about 14,200. Date: 11/01/2004 21.) Tinker-Toy gene fiddling | Russian roulette | bet on the final ... ... nanotechnology. Tinker Toy Folding Protein Picture. Heinrich Roder lab - Protein Folding Picture protein folding pictures Sign up ... www.vif.com/users/chris-m/medical/genome6.html google search for: symmetrically folding protein pictures The emerging picture of protein folding? is it correct? Today, the general picture of protein folding, is that it folds symmetricaly. But contrary to this commonly held picture of folding of proteins, (that it happens as a concerted motion) in which all parts fold simultaneously, all one needs to do is take a look at many womans labias, do they look like they were folded using a copy machine? symmetrically folding protein pictures The mathamatics (calculus) behind protein folding 1999 The National Academy of Sciences The 102-residue protein U1A has a symmetrically curved chevron plot which seems to result mainly from changes of the transition state. symmetrically packed purines folding protein pictures Results 1 - 10 of 10. JBC Online ... for p53 binding to response elements packed in chromatin ... GYYY, where R and Y are purines and pyrimidines ... The right domain is located symmetrically, so that its ... The overall lateral arrangement of the four p53 subunits with respect to the DNA loop comprises a novel nucleoprotein assembly that has not been reported previously in other complexes. We suggest that this kind of nucleoprotein superstructure may be important for p53 binding to response elements packed in chromatin and for subsequent transactivation of p53-mediated genes. He is deeply sceptical of the prevailing theories of evolution and the origin of life on Earth. A rare example of the use of mathematics to combine the two kinds of entropy is given in 'The Mystery of Life's Origin', published in 1984. Its authors acknowledge two kinds of entropy, which they call "thermal" and "configurational." To count the "number of ways" for the latter kind of entropy they use restrictions which they later admit to be unrealistic. They count only the number of ways a string of amino acids of fixed length can be sequenced. ...... Science is comfortable with saying ³I don¹t know². There are observered phenomena that have no cause. The classic example is the way random particles and antiparticles appear out of the vacuum and disappear again. Quantum physics is not determinitstic- it allows certain things to ³just happen² for no reason, but within a certain probability. Where do they come form, and what makes it happen? Why a proton, and not a neutron? Why now, and not a microsecond later? That question has no real answer, so there¹s no point asking it. Physicists have speculated that whole universes appear the same way- a ³negative universe² is created at the same time, so on a large enough scale there¹s still net nothingness. google search for: mini squid hawaii journal of science 'Bizarre' giant squid spotted in deep seas - The Honolulu ... ... Vecchione, first author of a study appearing today in the journal Science, said the only evidence of the squid comes from photographs and video images taken ... the.honoluluadvertiser.com/article/ 2001/Dec/21/ln/ln22a.html google search for: mini squid hawaii light emitting protein lenses 'Bizarre' giant squid spotted in deep seas The sightings were in the Pacific Ocean off O'ahu, the Atlantic and Indian oceans and in the Gulf of Mexico. The deepest sighting came at 15,534 feet — almost three miles below the surface — in the western Atlantic off the coast of Brazil. "Not only is this thing really bizarre, it seems to be fairly common in deep waters all over the world," said Vecchione. Little is known about creatures living in the deep waters of the world's oceans, he said. "This is the largest unexplored part of the Earth by far," said Vecchione. "I firmly believe that there is a lot of really weird stuff down there that we don't know about.... We are really ignorant about what lives on our own planet" at great depths. The photos show an animal with a relatively small head topped by large fleshy, collar-like fins. Extending from the base of the head are 10 wispy appendages sweeping out for up to 20 feet. Some of the appendages are sharply bent, as if at a joint. Some scientists reported seeing suckers on the upper part of the limbs. Suckers are a common feature of squid. The largest animal sighted was about 21 feet long, but most of that was legs and tentacles. [PDF] Does geometry limit squid growth? Journal of Cell Science Journal science january 2004 squid hawaii CBS News | Bright Squid Found In Hawaii | January 8, 2004 16:25:53 January 8, 2004 16:25:53, ... 8, 2004. ... by colonies of luminescent bacteria that live on the squids, the researchers report in Friday's issue of the journal Science. ... www.cbsnews.com/stories/2004/ 01/08/tech/main592194.shtml AP) A squid with a novel type of reflective plates that form a built-in light it may use to confuse predators has been discovered by scientists in Hawaii. While other luminous sea creatures are known, the reflective plates on the Hawaiian bobtail squid differ from those of other animals, according to researchers at Kewalo Marine Laboratory, University of Hawaii-Manoa. The light itself is provided by colonies of luminescent bacteria that live on the squids, the researchers report in Friday's issue of the journal Science. While reflective plates in many aquatic species are formed from chemicals Called purines, in this squid they were made from an unusual type of protein the researchers named reflectin. The chemical composition of that tissue is very unusual, agreed Michael Vecchione, director of the National Systematics Laboratory of the National Marine Fisheries Service. Crookes said the research team led by Margaret J. McFall-Ngai is now studying the relationship between the squids and the bacteria that produce the light. The bacteria and squids have a mutually beneficial relationship, Crookes said. Such relationships are common in nature, including beneficial bacteria in the human gut, she noted. Universal TAO System Sick and Tired Imagine your bloodstream and the inside of your body as a landscape or terrain. However, it is easy and common for body tissues to become too acid. This imbalance sets the stage for chaos. To say that health is a body terrain in acid/alkaline balance is to assume that it's also getting the raw materials (nutrients) it needs for maintenance and repair. In science, the acid/alkaline relationship is known as "pH". This pH balance in the body has a profound effect on the ecology of your terrain. Ecology is the relationship between organisms and their environment. In this case, the environment is your inner terrain, and the organisms are tiny (microscopic) forms of life. Some of these forms, such as those living in our digestive tract, are indispensable to life....... ...He used the term pleomorphism to define the growth cycle, and believed it to be a fundamental aspect of all illness. As profound as the change of caterpillar to a butterfly, this evolution is even more fantastic, since it can happen quit rapidly (some times in a matter of minutes!). The microbian doctrine also gave rise to the development of antibiotics, the first being penicillin in 1940. An antibiotic is the poisonous waste from one germ used in the attempt to kill another. Penicillin is the poison from a fungus. As a result of this development, most bacterial infections have apparently been "treatable" over the past 50 years. However, there seems to have been a price to pay for this convenient, and unscientific approach. And it is interesting to keep in mind that these tiny life forms, as well as the ones that are the main subject of this book-yeast, fungus and/or molds-are plants, not animals. Thus, we animals are essentially being taken over by vegetation. One of these is the existence in the interesting tract of necessary bacteria. There is a crucial, delicate balance between two general types, which we'll call "friendly" and "unfriendly" for convenience though it is not strictly accurate. With the substances they produce, the friendly ones help control the unfriendly ones. A major source of abuse of the friendly ones is antibiotics (exotoxins and mycotoxins, the waste products of bacteria, yeast and fungus), which reduce their numbers and allow a territorial takeover by the unfriendly group. (An antibiotic does not really kill bacteria. It simply makes them enter a different stage of their pleomorphic life cycle-like they duck out of the way. In any case, the antibiotic cannot balance the terrain condition, and in fact worsens it.) Taking enough poison to truly kill these powerhouses would kill you, because, in truth, they arise from part of your being. As emphasized, the primary diet of Y/F in our bodies is glucose for energy, plus fats and protein (even genetic matter, nucleic acids) for development growth. As these organisms feed, they produce was just like you do. Their "urine and feces" are called my toxins (myco = fungus; toxin = poison), and they are very poisonous to humans. This poisoning of the body mycotoxins is called mycotoxicosis. Being ac themselves, mycotoxins greatly worsen the acid caused by diet. They are released into the blood as w as inside cells. The blood poisoning results in more cell and tissue poisoning, and all of this further disturbs th microzymas, making us sick and tired. One very common mycotoxin that is particularly troublesome is acetaldehyde. It is quite detrimental itself, yet also breaks down to other products (called metabolites) including oxalic acid, lactic acid, uric acid, and alcohol. All are disruptive waste products of Y/F and are found in the blood and tissues of a compromised terrain. Compounding the situation is the fact that the presence of accatdehyde and other mycotoxins causes the liver to increase low density lipoprotein (LDL or so-called "bad" cholesterol) in the blood. This high-cholesterol complex is used to bind with toxins, thereby deactivating them. The binding process is often referred to as chelation. However, the resulting substance also has the tendency to become oxidized and stick to lesions (toxic damage) in the artery walls, producing atherosclerosis. Acetaldehyde can reduce strength and stamina, cause excessive fatigue, cloud thinking and take away ambition. One mechanism for these problems is that it directly destroys neurotransmitters, which are chemicals responsible for completing all nerve impulses. Needless to say, this is not a desirable situation! Another mechanism is that it can bind to the walls of red blood cells, making them less flexible and therefore less able to get into and through the capillaries of the circulatory system. This causes oxygen deprivation in the tissues. Added difficulty is that the liver converts aceta hyde to the mycotoxin alcohol. DNA (genetic material) may also be damage when excess acetaldehyde reacts with it, creating the following symptom pictures: pancreatitis (inflamed pancreas), cardiomyopathy (enlarged, weakend heart), dilated cardiomyopathy (heart muscle discord with an enlarged chamber), brain atrophy dement (wasting away of brain with loss of reasoning), atrophied brain with large ventricles (interior fluid spaces), jaundice, spider angina (broken surface blood vessels), enlarged spleen, stomach ulcers, esophagea varicosity (enlarged blood vessels in the esophagus) ascites (fluid in abdomen), cirrhosis, enlarged spleen tremor, bleeding tendency, easy bruising, ankle edema and reddening of the palms, just to name a few. .... I believe a similar thing happens in cancer and AIDS. The amount of uric acid and acetaldehyde produced by Y/F can be overhelming to the body. When acetaldehyde is converted into alcohol in the liver, the body is depleted of magnesium, sulfur, hydrogen and potassium, thus reducing cell energy. As mentioned, the body chelates uric acid and other toxins with fats, raising LDL cholesterol. In America one out of eight women will develop breast cancer, and the bread connection is everywhere. Japanese research links breast cancer with the ingestion of goods baked with yeast. It is known that in every breast cancer there are calcium oxalic acid, which is not made by humans but is made by most fungi. Oxalic acid is also a primary metabolite of uric acid, which means it is produced by a natural breakdown process. Uric acid is a primary waste product of brewer's yeast. ....... For example, I have seen, and recorded on video, rod microforms retrograding without any visible decomposition from 10 microns in length to the vicinity of. 1 micron. This research supports the very important postulate that the cell is not the smallest living biological unit, as promulgated by conventional medical science. In fact, a smaller biological unit is the imperishable microzyma, which is an organized, living being "of a special category without analogue, " said Becamp, who found them ready to become active in chalk deposits at least 11 million years old. I suggest a developmental cycle consisting of three macrostages: (1) a primitive stage comprising the repair protein complexes; (2) an intermediate, or bacterial, stage including filterable forms such as the cell-wall deficient forms described by Lida Mattman, Ph. D.; and (3) a culmination stage consisting of yeast and fungal phases, and then mold, the end phase. The usual course of development would be from microzyma to repair protein and then to bacterium, etc. However, under certain conditions, such as trauma for example, it is highly likely that the microzymas can skip the primitive stage and become bacteria directly. Although these transformations are as astounding as that of a larva to a butterfly, what is equally impressive under observation is the rapidity with which they can take place-in minutes, even seconds, sometimes. ...... The aforementioned causal (alarming) situation or modification of the medium, is chronic acid (pH imbalance) and oxygen deprivation in blood and tissues due to acid-forming foods, adv lifestyle, emotional stress, and environmental stress . This is not over simplification. Acidification biochemical signals a dead host to the microzyn while creating collapsed areas (dead zones) of colloidal system in the intercellular fluid. 2) and it is the primary physiological disease condition out of which the symptoms commonly come specific diseases arise. [Read more by clicking here] ------------------------------------------------------------------ The Uncertainty principal Coming soon! The uncertainty principal hunted down and reviewed on the Internet. How it could (and i would imagine it would) apply to diseases and protein folding itself? ------------------------------------------------------------------ And what about the difference between the basis of all computers today, namely the binary code of ie. (00100001) Capital "A" and the quaternary complex code of genetics ie. (AGTCCTAG....). What complexities can be drawn from that? Especially being that these 4 letters are not just codes, but are in reality - 4 complex amino acid proteins each with 3 dimensional shape! Proteins exist in a massive combinatorial space. Proteins are made up of amino acids, and amino acids are combinatorial, like the alphabet. In the same way twenty-six letters can be infinitely recombined, the twenty amino acids can make up a mind-boggling number of proteins. For long proteins -- those comprised of, say, one thousand or more amino acids -- the number of possible results approaches the number of atoms in the known universe. Protein Visualization: Seven Ways of Looking at a Protein Finally, there's the fact that proteins are not visible, not even in theory. This one is a corker. Because of the tremendous complexity in protein structure, and in the ways this 3-D structure can be characterized, visualization is the obvious tool for understanding protein -- but proteins cannot be seen, because they're too small to reflect light in any way the human eye can interpret. This leaves scientists using tools like X-rays to try to understand the structure, without being able to observe proteins directly. -------------------------------- Amazon Bio-technology books. jokes, food, ... Genome Matt Ridley New $11.20! How to Build a Time Machine P. C. W. Davies Bioinformatics for Dummies Jean-Michel Claverie Cartoon Guide to Genetics Larry Gonick The Immortal Cell ------------------- Adobe Photoshop Album Digital camera -------------- Nano Letters American Chemical ... New $1,220.13! Micro Nano Reed Business Info... New $215.15! Nano-bio-info Technology Convergence... Business Communica... New $499.95! Nano Et Micro Technologie Editions Hermes New $247.50! Amazon search for: Nano nanoparticles ------------------------------------- Genes Brain And Behavior Blackwell Publishing Ltd New $422.15! Bba Gene Structure And Expression Elsevier Bv Gene Therapy And Molecular Biology Intl Soc Gene Therapy Mole Bio Development Genes And Evolution Springer Verlag Germany Recombinant Dna - Gene Cloning & Sequencing Inst For Scientific Info gene ------------------- he X Factor Marianna Haun The Principles of Clinical Cytogenet... Steven L. Gersen The X in Sex David Bainbridge Handbook of Statistical Genetics D. J. Balding Chromatin and Gene Regulation Bryan M. Turner Chromosome Abnormalities and Genetic... R. J. M. Gardner The Calcutta Chromosome Amitav Ghosh New $11.20! Chromosome 6 Robin Cook Chromosome 6 Robin Cook Cellular structure - The Chromosome Chromosome ---------- New Aids drug has come along using a very small molicule! Aids virus has already become resistant to most currently used drugs. More to come soon! *********************************************************** Searched the web for: molecular genetic composition pictures Results 1 - 10 of about 29,600 3.) Genetic Composition | Unfolding and viewing the Protein ... Great new genetic self-decoding molecular bio-machine photos! Latest pictures in the gene self decoding bio-machine ... This shape, in turn, depends on its composition. ... www.vif.com/users/chris-m/medical/genome2.html ---------------------------- google search tr for: rna pictures arandi. 33,800 sonuçtan 11 - 20 15.) DNA-RNA MAKEUP ... Frontiers in Molecular Biology Gene Families: Studies of DNA, RNA, Enzymes and Proteins 02) 04:26 AM google.com 12-225-75-239.client.attbi.com rna dna pictures. ... www.vif.com/users/chris-m/medical/dna-rna.html ---------------------------- google searched the web for: using sed to get snippet of a file Results 1 - 10 of about 3,240 Neat SED and AWK ( sed awk ) scripts to clean up files and ... ... Search engine signatures Using SED AWK PERL S2P A2P to ... file and get rid of those nasty wasteful (filesize ... You must configure a code snippet which you install ... www.vif.com/users/chris-m/shopping-cart/ neat-sys-awk-tool.html - Entry Page: Page 43 ---------------------------- google searched the web for: bio technology pictures Results 21 - 30 of about 172,000 DNA-RNA MAKEUP ... dna pictures google.com Searched the web for: rna dna pictures\ Results 21 ... Doing everything with Blackberry ----- Amazon Bio-technology books ... www.vif.com/users/chris-m/medical/dna-rna.html ------------------------------- google searched the web for nano micro hole plant cells Results 21 - 30 of about 5,410 7.) Protein visualization Atlas of Protein Side-Chain Interactions. ... hole truth.html ( The Harvard Gazette ... Nano Et Micro Technologie Editions Hermes New ... search for: Nano nanoparticles ----- Genes ... www.vif.com/users/chris-m/medical/genome5.html HostName : 202.28.27.3 IP : 202.28.27.3 ------------------------------- google searched the web for: how meiosis work for dummies Results 11 - 20 of about 158 12.) CELL STRUCTURE ... Time Machine PCW Davies Bioinformatics for Dummies Jean-Michel ... I will not however, cover meiosis which is ... Columbia University points out, "enzymes work so well ... www.vif.com/users/chris-m/medical/cell-structure.html - HostName : fw1.nmh.org IP : 209.107.68.193 Last Visit : New Country: US Organisation Browser: MSIE [Win XP] Page Views: 2 Daily Visits: 1 Visit Length: 5 minute(s) 24 second --------------------------------------- google searched the web for: "cell division" for dummies Results 11 - 20 of about 178 CELL STRUCTURE ... How to Build a Time Machine PCW Davies Bioinformatics for Dummies Jean-Michel Claverie Cartoon Guide to Genetics Larry ... Cells DNA RNA Chromosomes Cell Division ... www.vif.com/users/chris-m/medical/cell-structure.html --------------------------------------- google searched the web for: awk scripts Results 11 - 20 of about 136,000 Neat SED and AWK ( sed awk ) scripts to clean up files and ... November 2003 google Searched the web for: substr in awk scripts substr in awk scripts Results 1 - 10 of about 8,780 In November on the 28th., we were found #2 ... www.vif.com/users/chris-m/shopping-cart/ neat-sys-awk-tool.html Entry Page: Page 43 --------------------------------------- Searched the web for "protein side-chain interactions Results 1 - 10 of about 520 4.) Protein visualization Atlas of Protein Side-Chain Interactions. ... ... Atlas of Protein Side-Chain Interactions and Visualization! Do visit the protein folding visualization books and links at: This Site! ... www.vif.com/users/chris-m/medical/genome5.html Wed 14 Jan,14:23:30 sc267651.gs.myharris.net HostName : sc267651.gs.myharris.net IP : 158.147.16.196 Last Visit : New Country: US Network Browser: MSIE [Win NT] Page Views: 2 Daily Visits: 1 Visit Length: 2 minute(s) 44 second Entry Page: genome5 Exit Page: cell-structure.html Referring URL: http://www.google.com/search?hl=en&ie=UTF-8&oe=UTF-8&q=%22protein+side-chain+interactions% Navigation Report Time Page 14:23 genome5 14:26 cell-structure.html --------------------------------------- NEW! XARA site updater NEW! XARA "hit tracker program" NEW XARA "Real Tracker" See who's coming on your site! NEW! XARA "sliding messages effect" Searched the web for: genetics services affiliate program . Results 1 - 10 of about 71,000 Jackson Laboratory Research Affiliates For more information about becoming a member of The Jackson Laboratory Research Affiliates Teresa Chu, Ph.D. Scientific Liaison, The Research Affiliates Program The Jackson Laboratory 610 Main Street Bar Harbor, ME 04609 Tel: (207) 288-6775 Fax: (207) 288-6152 Email: tchu@jax.org COURSES AVAILABLE SEARCH THEIR DATABASES ----------------------------------- Searched the web for DNA RNA tutorial . Results 11 - 20 of about 27,400 DNA-RNA MAKEUP ... Molecular Biotechnology 1555811361:Product Link on Barnes & Noble.com. DNA RNA Tutorials (Tulane University New Orleans LA). The central dogma of Biology: ... www.vif.com/users/chris-m/medical/dna-rna.html genome.icmb.utexas.edu IP : 146.6.213.74 Last Visit : New Country: US Educational Wed 28 Jan,14:48:39 genome.icmb.utexas.edu 1 New Win XP Yale University: CNS language tutorials: C shell scripts documentation The term "generate" explained Generating and manipulating the molecular topology A simple protein A protein with a ligand and an ion A protein with capping groups + ion + water A simple DNA duplex A simple RNA duplex A hybrid DNA/RNA duplex Phasing by Isomorphous Replacement (SIR/MIR) Flowchart of SIR/MIR phasing protocol (PDF format) Universita of Manitoba: TUTORIAL: DATABASE SIMILARITY SEARCHES This tutorial assumes you already know how to retrieve DNA sequences from GenBank and protein sequenes from PIR. Example: Antifreeze Proteins Note: DNA vs. DNA searches are far less sensitive than protein vs. protein searches. DNA searches only work for closely-related sequences. -------------------- Wed 28 Jan,14:18:21 fw2.pittstate.edu 2 New Win 2000 HostName : fw2.pittstate.edu IP : 198.49.81.32 Last Visit : New Country: US Educational Browser: MSIE [Win 2000] Page Views: 2 Daily Visits: 1 Visit Length: 0 minute(s) 39 second Entry Page: genome Exit Page: dna-rna.html Referring URL: msn search for: Books+on+GMO "The Ultimate Gamble" MSN Search Preview shows VIF Internet and links to: genome.html Navigation Report Time Page 14:18 genome 14:19 dna-rna.html ------------------------------ Searched the web for composition human feces genetic material . Results 1 - 10 of about 4,420 #4.) www.vif.com/users/chris-m/medical/genome2.html genetics testing ------------------------------- Searched the web for "cryptanalysis of a5/2" . Results 1 - 6 of about 11 Last Minute Holiday Gift Ideas ... software enforcement of export controls. The Real-Time Cryptanalysis of A5/2, David Wagner et al. They reverse engineered and cracked ... www.vif.com/users/chris-m/e-comm7.html wwwgate32.motorola.com IP : 136.182.2.222 ------------------------------- scripts genbank program Biology Bioinformatics Software google searched for: perl scripts genbank Results 1 - 10 of about 4,630 google search for: awk scripts genbank Results 1 - 10 of about 286 google search for: awk scripts genbank As you can see with this google search, much of the valuable data generated by the HGP and other endevors, even though there, it is however something else to make sense of. Many scripts have and continue to be written to organize the data into meaningfull structure, much like the data actually represents ie. shape and dynamic action/reaction or growth / reshaping and interaction with their sub-molecular co-factors/co-habitors ie. their immediate environment. some of these scripts are written in C, Shell scripts, Perl, BioPerl, Awk, sed, or even simple grep to pull certain elements from a database. Bioinformatical analysis and prediction regulatory gene expression proteins from Human proteome Proteome and Protein Knowledgebases Gene Ontology (GO) Another attractive possibility is making FASTA similarity searches over selected proteome organisms as well as using SRS/EBI Another important proteome resource is IPI (International Protein Index). IPI catalogues non-redundantly all proteins sequences of SWISS-PROT/TREMBL RefSeq Ensembl SWISS-PROT offers the most reliable and fully known proteins and peptides sequenced and characterized in several organisms. TrEMBL, standing for Translated European Molecular Biology Lab (sequences) is inferred from nucleic acid sequences from EMBL not yet incorportated and to be passed soon to SWISS-PROT, acting in the meanwhile as a supplement. Recently, there is also a another resource TrEMBLNEW that feeds both SWISS-PROT and TrEMBL in the end but using a different methodology. TranScout is a program developed for detecting and analysing conserved motifs of protein regulatory sequences. TranScout is an built over an extension to TRANSFAC a database of transcription factors. In that site, there is an analog program to Transcout named MatInspector Is a perl program / script, which relies upon TRANSFAC classification, TranScout uses its own classification. If interested in further information on TranScout you may look up at its web help transcout help There also you can find a classification FIND Classification of transcription factors considered in TranScout program. SSV (star separated value), a CSV separated by * , for avoiding any entry with commas or semicolons inside any of the fields. " Through all the chapters of this document, the steps taken from raw proteome biodata (sequence and annotation) until web publising of results and analysis derived from TranScout have been faithfully described noting their biological implications. Technical informatics solutions to the proposed biological problems have been included along the text or extended in the appendices, and even when possible, proposed better implementation options to be used in the future or in a more automatizated protocol have been given. Upcoming results in TrSDB will represent another good resource among the excellent BioKnowledgeBases we can surf on the Web. BioPerl Bioperl is an Open Collaborative effort to simplify Bioinformatics tasks with Perl. It consists of a collection of module classes concerning most usual a bioinformaticist must face; such as sequence database retrieval, field extraction, pairwise or multiple alignment, plus different kinds of file type parsings and conversions. Bioperl is within the umbrella of Open Bioinformatics Foundation, which englobates several projects BioJava BioPython BioRuby ENSEMBL EMBOSS ENSEMBL, an automated genome sequence database works fully based upon Bioperl. One of ENSEMBL maintainers, Ewan Birney, is also one of the major Bioperl collaborators. At beginnings 2002 Bioperl 1.0 has been finally been released after about 7 years of the creation of Bioperl group. Bioperl package may also include a set of database SQL utilities. Definitively, Bioperl is an outstanding model and a very helpful tool for designing an any-scale work in Bioinformatics. At that site you can read an enjoying article on How Perl saved the Human Genome Project (http://bioperl.org/GetStarted/tpj_ls_bio.html). Finally, remembering Perl's famous motto, Perl make easy things easy, and difficult things possible; now with Bioperl, much easier than before in Bioinformatics (or much more possible.) ------------------------------------------------ If you have a Genomic or biotech product, service or program you would like to advertise with us, please contact us here @: OR Visit our affiliate info site at: submit-it affiliate programs Searched the web for: genetics services affiliate program . Results 1 - 10 of about 71,000 Jackson Laboratory Research Affiliates For more information about becoming a member of The Jackson Laboratory Research Affiliates Teresa Chu, Ph.D. Scientific Liaison, The Research Affiliates Program The Jackson Laboratory 610 Main Street Bar Harbor, ME 04609 Tel: (207) 288-6775 Fax: (207) 288-6152 Email: tchu@jax.org COURSES AVAILABLE SEARCH THEIR DATABASES ----------------------------------- Searched the web for DNA RNA tutorial . Results 11 - 20 of about 27,400 DNA-RNA MAKEUP ... Molecular Biotechnology 1555811361:Product Link on Barnes & Noble.com. DNA RNA Tutorials (Tulane University New Orleans LA). The central dogma of Biology: ... www.vif.com/users/chris-m/medical/dna-rna.html genome.icmb.utexas.edu IP : 146.6.213.74 Last Visit : New Country: US Educational Wed 28 Jan,14:48:39 genome.icmb.utexas.edu 1 New Win XP Yale University: CNS language tutorials: C shell scripts documentation The term "generate" explained Generating and manipulating the molecular topology A simple protein A protein with a ligand and an ion A protein with capping groups + ion + water A simple DNA duplex A simple RNA duplex A hybrid DNA/RNA duplex Phasing by Isomorphous Replacement (SIR/MIR) Flowchart of SIR/MIR phasing protocol (PDF format) Universita of Manitoba: TUTORIAL: DATABASE SIMILARITY SEARCHES This tutorial assumes you already know how to retrieve DNA sequences from GenBank and protein sequenes from PIR. Example: Antifreeze Proteins Note: DNA vs. DNA searches are far less sensitive than protein vs. protein searches. DNA searches only work for closely-related sequences. -------------------- Wed 28 Jan,14:18:21 fw2.pittstate.edu 2 New Win 2000 HostName : fw2.pittstate.edu IP : 198.49.81.32 Last Visit : New Country: US Educational Browser: MSIE [Win 2000] Page Views: 2 Daily Visits: 1 Visit Length: 0 minute(s) 39 second Entry Page: genome Exit Page: dna-rna.html Referring URL: msn search for: Books+on+GMO "The Ultimate Gamble" MSN Search Preview shows VIF Internet and links to: genome.html Navigation Report Time Page 14:18 genome 14:19 dna-rna.html ------------------------------ Searched the web for composition human feces genetic material . Results 1 - 10 of about 4,420 #4.) www.vif.com/users/chris-m/medical/genome2.html genetics testing ------------------------------- Searched the web for "cryptanalysis of a5/2" . Results 1 - 6 of about 11 Last Minute Holiday Gift Ideas ... software enforcement of export controls. The Real-Time Cryptanalysis of A5/2, David Wagner et al. They reverse engineered and cracked ... www.vif.com/users/chris-m/e-comm7.html wwwgate32.motorola.com IP : 136.182.2.222 ------------------------------- Searched the web for david protein visualization . Results 1 - 10 of about 33,000 6.) Protein visualization Atlas of Protein Side-Chain Interactions. ... Do visit the protein folding visualization books and links at: This ... Steven L. Gersen The X in Sex David Bainbridge Handbook of ... and here: Protein Folding site. ... www.vif.com/users/chris-m/medical/genome5.html DAVID: ( Database for Annotation, Visualization, and Integrated Discovery ) A previous version of this manuscript was made available before peer review at Subject areas: Bioinformatics, Genome studies Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://www.david.niaid.nih.gov) addresses this need via four web-based analysis modules: 1) Annotation Tool - rapidly appends descriptive data from several public databases to lists of genes; 2) GoCharts - assigns genes to Gene Ontology functional categories based on user selected classifications and term specificity level; 3) KeggCharts - assigns genes to KEGG metabolic processes and enables users to view genes in the context of biochemical pathway maps; and 4) DomainCharts - groups genes according to PFAM conserved protein domains. Genechip Analysis Details of the experimental, RNA preparation, and Genechip hybridization procedures, along with details of the chip-to-chip normalizations and statistical analysis of differential gene expression are provided in Cicala et al., [9]. Briefly, primary human peripheral blood mononuclear cells (PBMCs) and monocyte-derived macrophages were incubated for 16 hours with HIV-1 envelope protein (gp120). High-density oligonucleotide microarrays (Affymetrix HU-95A GeneChip) were used to monitor gp120 induced transcriptional events. System Architecture and Maintenance An automated procedure written in Microsoft Visual Basic (VB) 6.0 updates DAVID weekly with the following procedures: (i) call a series of Perl and Java applications that download public data through anonymous file transfer protocols (FTP) (Table 1); (ii) unpack and parse desired annotation data; (iii) create tab-delimited data files ready for database import; and (iv) import data into an Oracle 8i relational database management system (RDBMS) using Oracle's SQL*Loader application. An Apache webserver and Java Server Pages (JSP) access the database using JavaBeans and the structured query language (SQL). LocusLink numbers for Affymetrix probe sets are derived from NetAffx [10] or University of Michigan associations [11]. :: http://www.david.niaid.nih.gov DAVID's Annotation Tool, GoCharts, KeggCharts, andDomainCharts combine to provide high-throughput methods for functional annotation and biological discovery, all of which can be accessed via the internet at http://www.david.niaid.nih.gov. The Annotation Tool efficiently appended annotations to 402 genes in less than twelve seconds and provided functional summaries and links to external data sources, all of which could be downloaded to a users personal workstation for further analysis. Complementary features including graphic visualizations of functional categories, conserved protein domains, and biochemical pathways were provided by GoCharts, DomainCharts, and KeggCharts that quickly led to the identification of stress response cytokines and protein kinases as major functional categories modulated by HIV-1 envelope proteins. This analysis supports the findings reported by the original authors and illustrates the utility of DAVID in the rapid annotation and analysis of large datasets commonly generated by high-throughput expression profiling. ------------------------------- next page» <<  Back   2 of 8 Feedback  |  About Us  |  Search site  |  Copyright © MEYCOM