Freethought & Rationalism Archive

Oolon Colluphid · 09-03-2002, 03:18 AM

Monkenstick, thanks for that, I'm sure it's fascinating and useful.... but you couldn't translate it into English please, could you?

If I don't quite follow it, I'm damn sure Chris Groves won't be able to!

Cheers, Oolon

[ September 03, 2002: Message edited by: Oolon Colluphid ]</p>

monkenstick · 09-03-2002, 03:54 AM

I just had a better idea - comparing whole mitochondrial genomes!

Quote:

CLUSTAL W (1.82) Multiple Sequence Alignments

Sequence format is Pearson
Sequence 1: cow 16338 bp
Sequence 2: kangaroo 16896 bp
Sequence 3: human 16569 bp
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 70
Sequences (1:3) Aligned. Score: 72
Sequences (2:3) Aligned. Score: 66
Guide tree file created: [/ebi/extserv/old-work/34679.11486.dnd]
Start of Multiple Alignment
There are 2 groups
Aligning...
Group 1: Sequences: 2 Score:242477
Group 2: Sequences: 3 Score:226703

.....

Sequences (cow:human) Aligned. Score: 72
Sequences (kangaroo:human) Aligned. Score: 66
Alignment Score 228147
CLUSTAL-Alignment file created [/ebi/extserv/old-work/34679.11486.aln]

72 percent homology vs 66 percent

human DNA is closer to cow DNA than to kangaroo DNA

[ September 03, 2002: Message edited by: monkenstick ]</p>

Albion · 09-03-2002, 11:10 AM

Interesting - pretty much goes to show that if you pick and choose the details to suit you, you can demonstrate anything. Then all you have to do is "forget" to mention the ones that didn't give the results you wanted.

lpetrich · 09-03-2002, 12:48 PM

Monkenstick, I wonder how automated one can make that analysis procedure; I'm half-thinking of trying some myself. Ideally, one might want to write a Unix shell script that grabs the files and then passes them to some command-line programs.

I have AppleBSD, a.k.a. MacOS X, and I've successfully built and run "phylip" at home. I'm worried about how much editing of intermediate results that one might have to do, so one program's output can be used as another one's input.

monkenstick · 09-03-2002, 03:27 PM

hey lpetrich, theres an absolutely fantastic website/program for bioinformaticians;

<a href="http://www.angis.org.au/new/bioinformatic/biomanager.html" target="_blank">http://www.angis.org.au/new/bioinformatic/biomanager.html</a>

you can do all sorts of stuff with it, and its automated - give it some tasks to do, come back the next day and they're all done and saved on your account. when you click on the output of one program, it lists every program which can use that output as an input - you simply have to choose one then by clicking on it.

I had access to it last semester as part of a bioinformatics course, but not anymore

[ September 03, 2002: Message edited by: monkenstick ]</p>

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09-03-2002, 03:18 AM	#31
Oolon Colluphid Contributor Join Date: Sep 2000 Location: Alibi: ego ipse hinc extermino Posts: 12,591	Monkenstick, thanks for that, I'm sure it's fascinating and useful.... but you couldn't translate it into English please, could you? If I don't quite follow it, I'm damn sure Chris Groves won't be able to! Cheers, Oolon [ September 03, 2002: Message edited by: Oolon Colluphid ]</p>

09-03-2002, 11:10 AM	#33
Albion Veteran Member Join Date: Jul 2002 Location: US east coast. And www.theroyalforums.com Posts: 2,829	Interesting - pretty much goes to show that if you pick and choose the details to suit you, you can demonstrate anything. Then all you have to do is "forget" to mention the ones that didn't give the results you wanted.

09-03-2002, 12:48 PM	#34
lpetrich Contributor Join Date: Jul 2000 Location: Lebanon, OR, USA Posts: 16,829	Monkenstick, I wonder how automated one can make that analysis procedure; I'm half-thinking of trying some myself. Ideally, one might want to write a Unix shell script that grabs the files and then passes them to some command-line programs. I have AppleBSD, a.k.a. MacOS X, and I've successfully built and run "phylip" at home. I'm worried about how much editing of intermediate results that one might have to do, so one program's output can be used as another one's input.

09-03-2002, 03:27 PM	#35
monkenstick Regular Member Join Date: Jul 2002 Location: Australia Posts: 214	hey lpetrich, theres an absolutely fantastic website/program for bioinformaticians; <a href="http://www.angis.org.au/new/bioinformatic/biomanager.html" target="_blank">http://www.angis.org.au/new/bioinformatic/biomanager.html</a> you can do all sorts of stuff with it, and its automated - give it some tasks to do, come back the next day and they're all done and saved on your account. when you click on the output of one program, it lists every program which can use that output as an input - you simply have to choose one then by clicking on it. I had access to it last semester as part of a bioinformatics course, but not anymore [ September 03, 2002: Message edited by: monkenstick ]</p>

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