Slashdot Mirror

The convention is to write in the 5' to 3' direction and usually the sense strand. Unless I'm getting things backwards again (and I often am, can't keep left and right straight either) 3-TAC-5 in the antisense strand is what is actually used to copy the mRNA transcript, which is 5-AUG-3, the same as the sense strand 5-ATG-3. The t-RNA has UAC which corresponds to it.

So, unless I'm once again confused, that would be two types of backward.

Anyway, there is no message in any frame, nor on the complementary strand.

http://www.expasy.ch/tools/dna.html

5'3' Frame 1

EYIAH-YIET

5'3' Frame 2

NTSHISILR

5'3' Frame 3

IHRTLVY-D

3'5' Frame 1

SLNILMCDVF

3'5' Frame 2

VSIY-CAMY

3'5' Frame 3

SQYTNVRCI

and reversing the sequence, in case it was written 3-5 also had nothing

TCA GAG TTA TAT GAT TAC ACG CTA CAT AAG

5'3' Frame 1

SELYDYTLHK

5'3' Frame 2

QSYMITRYI

5'3' Frame 3

RVI-LHAT-

3'5' Frame 1

LM-RVII-L-

3'5' Frame 2

LCSV-SYNS

3'5' Frame 3

YVACNHITL

I also did a quick blast search of the human genome and came up with no hits. I started trying to set the parameters to allow for mismatches (I don't use it all that often) when I realized that I'm probably completely missing the joke.

...The joke is on me, isn't it?

I am not sure why simply because it is about one of many available tools, the post is out of place on Slashdot. I am not a member of a huge biochem or medical lab, but I am trying to learn and use biochemistry, so I can use every bit of help.

It's out of place because the announcement is somewhat akin to posting a front page article when some guy releases version 0.1 of a new text editor onto Sourceforge. It's been done a million times before, and it doesn't cover any new ground. It isn't even interesting to people who don't use text editors.

That said, if you're really trying to get a handle on biochem and molecular biology (and the bioinformatics that goes along with it), almost all up to date textbooks on the subject include a section (or more) on bioinformatics. In 2006, knowing how to perform basic analysis on your DNA or protein sequence is just about as important as understanding the concept of a gene, or how the complementary nature of DNA works. If the textbooks you currently have are a little out of date, take a look around the library and grab something more recent. There are also plenty of bioinformatics and sequence analysis textbooks on the shelves now.

If you're looking for some places to get started, (and I think someone has already mentioned these), try ExPASy . Although it's more protein oriented, it has an extensive list of links to a very broad cross-section of bioinformatics and sequence analysis tools (along with some tutorials). Also take a look at NCBI, which not only has a range of important tools (like BLAST), but also PubMed. In a similar vein, also explore the EBI site which has another extensive set of tools and databases.

Since you ask, some of the stuff that I commonly use for bog-standard molecular biology tasks (in addition to the links above) includes PlasMapper (finds restriction sites and generates tasteful plasmid maps) and the New England Biolabs site which has some similar tools (NEBcutter, for example), but also handy information on all the restriction enzymes themselves.

If you're into writing bioinformatics applications yourself, start by looking at something like BioPerl. Just using Perl as an example (since it's very popular in biology), there are pre-existing libraries, all fully open sourced and Free(tm), which do things like reverse translation and interfacing with analysis tools like BLAST already.

That's just the tip of the iceberg. Anyone getting started in molecular biology will discover these kinds of sites very quickly. They're mentioned in the textbooks, they're easily found with Google, and they'll be revealed after a 2 minute conversation with anyone working in the field. That's what make this story so pointless. There's nothing new here. It's all been done before, and done 500 times before at that. Even outsiders from other sciences will discover this kind of stuff within a day or two if they're actually serious.

But nobody is going to go to the trouble of synthesyzing an Ebola virus because it's too much trouble and there's a better way to turn it into a Weapon of Mass Destruction (WMD). Ebola has just seven genes and only one of these produces the substance that causes the 90% fatality rate - Ebola glycoprotein. The gene for this protein has already been isolated and put in a common cold virus!!!

"...Nabel's team worked with intact blood vessels taken from people and animals. The researchers infected those cells with a cold virus they had engineered to carry the Ebola glycoprotein gene. Within 48 hours, massive numbers of endothelial cells began to die and the blood vessels became leaky. Such effects could lead to the internal and external bleeding caused by Ebola...."

Kinda makes you wonder where ol' Nabel's virus is now, huh? Hope it's safely in the bottom of his lab freezer. But inserting the Ebola glycoprotein in a bacterium (as opposed to a virus) is basically a science fair project these days, so ANYBODY can get in on the fun. Who knows, the next Jack in the Box E Coli scare may very well be a version with an Ebola gene in it. The basic data you need for such a project is onlione at the SWISS-PROT database in Switzerland; just enter ebola in their search engine and see for yourself. The specific data for Ebola glycoprotein is here, and in case that gets slashdotted, the relevant sequence data info is as follows:

MGVTGILQLP RDRFKRTSFF LWVIILFQRT FSIPLGVIHN STLQVSDVDK LVCRDKLSST NQLRSVGLNL EGNGVATDVP SATKRWGFRS GVPPKVVNYE AGEWAENCYN LEIKKPDGSE CLPAAPDGIR GFPRCRYVHK VSGTGPCAGD FAFHKEGAFF LYDRLASTVI YRGTTFAEGV VAFLILPQAK KDFFSSHPLR EPVNATEDPS SGYYSTTIRY QATGFGTNET EYLFEVDNLT YVQLESRFTP QFLLQLNETI YTSGKRSNTT GKLIWKVNPE IDTTIGEWAF WETKKTSLEK FAVKSCLSQL YQTEPKTSVV RVRRELLPTQ GPTQQLKTTK SMASENSSAM VQVHSQGREA AVSHLTTLAT ISTSPQSLTT KPGPDNSTHN TPVYKLDISE ATQVEQHHRR TDNDSTASDT PSATTAAGPP KAENTNTSKS TDFLDPATTT SPQNHSETAG NNNTHHQDTG EESASSGKLG LITNTIAGVA GLITGGRRTR REAIVNAQPK CNPNLHYWTT QDEGAAIGLA WIPYFGPAAE GIYIEGLMHN QDGLICGLRQ LANETTQALQ LFLRATTELR TFSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF VDKTLPDQGD NDNWWTGWRQ WIPAGIGVTG VIIAVIALFC ICKFVF

Any genetic engineer worth her salt should be able to take this data and create a Ebola / E Coli hybrid plasmid with the help of this data and a friendly mail order supplier of synthetic DNA...

But nobody is going to go to the trouble of synthesyzing an Ebola virus because it's too much trouble and there's a better way to turn it into a Weapon of Mass Destruction (WMD). Ebola has just seven genes and only one of these produces the substance that causes the 90% fatality rate - Ebola glycoprotein. The gene for this protein has already been isolated and put in a common cold virus!!!

"...Nabel's team worked with intact blood vessels taken from people and animals. The researchers infected those cells with a cold virus they had engineered to carry the Ebola glycoprotein gene. Within 48 hours, massive numbers of endothelial cells began to die and the blood vessels became leaky. Such effects could lead to the internal and external bleeding caused by Ebola...."

Kinda makes you wonder where ol' Nabel's virus is now, huh? Hope it's safely in the bottom of his lab freezer. But inserting the Ebola glycoprotein in a bacterium (as opposed to a virus) is basically a science fair project these days, so ANYBODY can get in on the fun. Who knows, the next Jack in the Box E Coli scare may very well be a version with an Ebola gene in it. The basic data you need for such a project is onlione at the SWISS-PROT database in Switzerland; just enter ebola in their search engine and see for yourself. The specific data for Ebola glycoprotein is here, and in case that gets slashdotted, the relevant sequence data info is as follows:

MGVTGILQLP RDRFKRTSFF LWVIILFQRT FSIPLGVIHN STLQVSDVDK LVCRDKLSST NQLRSVGLNL EGNGVATDVP SATKRWGFRS GVPPKVVNYE AGEWAENCYN LEIKKPDGSE CLPAAPDGIR GFPRCRYVHK VSGTGPCAGD FAFHKEGAFF LYDRLASTVI YRGTTFAEGV VAFLILPQAK KDFFSSHPLR EPVNATEDPS SGYYSTTIRY QATGFGTNET EYLFEVDNLT YVQLESRFTP QFLLQLNETI YTSGKRSNTT GKLIWKVNPE IDTTIGEWAF WETKKTSLEK FAVKSCLSQL YQTEPKTSVV RVRRELLPTQ GPTQQLKTTK SMASENSSAM VQVHSQGREA AVSHLTTLAT ISTSPQSLTT KPGPDNSTHN TPVYKLDISE ATQVEQHHRR TDNDSTASDT PSATTAAGPP KAENTNTSKS TDFLDPATTT SPQNHSETAG NNNTHHQDTG EESASSGKLG LITNTIAGVA GLITGGRRTR REAIVNAQPK CNPNLHYWTT QDEGAAIGLA WIPYFGPAAE GIYIEGLMHN QDGLICGLRQ LANETTQALQ LFLRATTELR TFSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF VDKTLPDQGD NDNWWTGWRQ WIPAGIGVTG VIIAVIALFC ICKFVF

Any genetic engineer worth her salt should be able to take this data and create a Ebola / E Coli hybrid plasmid with the help of this data and a friendly mail order supplier of synthetic DNA...

I agree. "Open Source" in biology is more the rule than the exception.l I have been astounded by the FREE resources out there available for anyone to use! Databases like Genbank and Swiss-Prot are invaluable to modern molecular work. Pedro's Biomolecular Tools is just a sample of the plethora of free resources available today.

Incidentally, I can't recommend Ensembl highly enough. Not only have I been able to significantly further my research with their tools, but they have open-sourced the entire code behind their site! And the documentation is even in Wiki! I really think what they have done is incredible and should be one of the first projects anyone mentions when expounding the virtues of open-source software as well as sharing information in the field of Biology.

-Ryan

The starting point for this has to be the classic Boehringer Mannheim "Biochemical Pathways" charts which you can access on the Web here and here. Just click on one of the squares and it will present you with a blow-up of that section of the chart. These are also available as HUGE wallcharts on paper you can order from here. Amazing, ain't it? How the proteins produced by DNA manage to work together as catalysts to create the chemicals needed to form an organism is almost totally unknown, yet by definition it is a cellular automaton problem! To read up on all of this stuff, start with this, then for more details go here and here. After you've skimmed all of the above, pick a site from here or here or here and keep going. It never stops.

The starting point for this has to be the classic Boehringer Mannheim "Biochemical Pathways" charts which you can access on the Web here and here. Just click on one of the squares and it will present you with a blow-up of that section of the chart. These are also available as HUGE wallcharts on paper you can order from here. Amazing, ain't it? How the proteins produced by DNA manage to work together as catalysts to create the chemicals needed to form an organism is almost totally unknown, yet by definition it is a cellular automaton problem! To read up on all of this stuff, start with this, then for more details go here and here. After you've skimmed all of the above, pick a site from here or here or here and keep going. It never stops.