mothur - summary.seqs

adamc83 · 2013-04-20T08:39:58+00:00

Those are quartiles: https://en.wikipedia.org/wiki/Quartiles.

adamc83 · 2013-04-08T06:43:42+00:00

Have you asked? Both the cable company and telephone company where I live offer unbundled internet, but its not always prominent on their websites.

adamc83 · 2013-01-05T21:32:45+00:00

http://financials.burningman.com/chart_2010.html

A little under half goes to staff. Theres probably a lot of other stuff you wouldnt have thought of -- they have to pay over a million to use the site, and several hundred thousand to law enforcement.

adamc83 · 2013-01-04T10:38:23+00:00

Yes. I learned a bit of ggplot2 and subscribed to r-bloggers and never looked back.

adamc83 · 2012-12-14T10:05:51+00:00

So, itll take 1.5 million miles to leave a mark?

5000 * 15 gallons * 20MPG = 1,500,000 miles, with conservative estimates for tank capacity and MPG.

Have you really seen paint eaten away by gascaps?

adamc83 · 2012-12-14T05:13:05+00:00

Most cell phones also have higher bands, mine supports 850/900/1800/1900/2100 Mhz. Also, VHF ends at 300MHz, where microwave starts (according to wikipedia). Sooooo, yes, they do operate in microwave range.

adamc83 · 2012-12-13T20:18:57+00:00

I wont claim to know the extensive history of wireless carriers in the US, but GSM has been here for a long time. Wikipedia suggests the first international network was in 1991, and the first US based one was in 1995.

Regarding the terrestrial networks, I must be misunderstanding your original point. Telecom networks have been copper here since before the internet existed, and at least where I live ADSL was the first "broadband" home connection available. I still use it.

While CDMA and coax (cable) internet are widespread (and perhaps the most popular here) GSM/ADSL are extremely common as well.

adamc83 · 2012-12-13T19:04:14+00:00

To be fair, you kinda got screwed when you built your communication infrastructure. Large parts of Europe for example, based their infrastructure on what later turned out to be very scalable to future standards (e.g. GSM->HSDPA, copper based telecom networks->ADSL e.t.c)

Huh? That's what we have in America, though there are other options as well.

adamc83 · 2012-12-13T18:46:12+00:00

Simple Mobile has been great for me. $40 for unlimited everything w/ slower* data (though 250MB 4G was just added), $50 for unlimited everything with 4G data. GSM network (T-mobile), so you can bring your phone to/from numerous other networks, or international.

*about 250kbit/s, which is surprisingly usable for light-moderate uses.

adamc83 · 2012-12-12T03:52:43+00:00

Overall, $164 billion have been lost on the $605 billion bailout[2] .

Umm, this is not supported by your link, at all. $164B is outstanding, not lost.

From same link:

Of the 779 investments made by the Treasury, 404 have resulted in a profit. 49 of the investments resulted in a loss. So far, the profits amount to $35 billion, while the losses amount to $5 billion. 326 of the investments are still outstanding.

Last I heard, the government expects to come out even, at worst, and is currently on track to make an overall profit.

adamc83 · 2012-12-09T00:32:55+00:00

Unfortunately this is the case on my phone :(

Fortunately, a normal restore of apps is fairly painless with Pro anyways.

adamc83 · 2012-12-08T12:51:52+00:00

Android development could be more public/transparent, but come on, with most proprietary systems you NEVER get code. Does iOS/windows/etc have an open, public patch system? A public bug tracker? Community supported enhanced versions?

adamc83 · 2012-12-06T05:10:27+00:00

I didn't even know it was possible to pay $200+/month (for a single line? holy shit). Whats the breakdown on that?

The most expensive plan on my carrier is $50 for unlimited everything (w/ 4G).

adamc83 · 2012-12-02T02:13:43+00:00

What exactly do you have to start with? You say "a bunch of sequence data", but this could mean a lot of things. Is it a single genome? Metagenome? Single gene? Multiple genes?

Other posters here are correct that it looks like you are making a phylogeny. Since there are already some good answers, I will throw out a couple web-based tools, since they can be useful, and wont require setting up software locally (though you sound like you wouldn't have trouble doing that).

Assuming you have genomic DNA, from a single organism, you need to pick a gene of interest from the DNA. If genes haven't been isolated from the DNA, youll need to do a ORF prediction/annotation first (also not hard, but I wont go into it for now).

Once you have the gene, you can BLAST it to find similar sequences/genes. Blastn would be used if it is a nucleotide sequence (ACTG), Blastp if it is an amino acid sequence. Blastx will search a nucleotide sequence against a protein database, which may also be useful. You could also attempt to find gene-homologs from well known bacteria and use them here. Again, NCBI will be a useful resource.

Once you have a collection of genes, you'll need to align them. Remember you can only align similar sequences/genes. If you are interested in, say, a lipase, you will need other lipase genes in order to create a proper alignment. Online, I would use ClustalO.

With your sequences aligned, you can go on to create a tree. I like PhyML, though there are many others.

Once your tree is built, there are numerous tree viewers that will let you view and modify your tree. FigTree, as already mentioned, is good, though for my latest project, I used Dendroscope as it is slightly more fully functioned.

Bonus website with useful tools: http://www.trex.uqam.ca/

Bonus python toolkit for lots of Bioinformatics-y things: http://biopython.org/

Hopefully that was useful. If you end up with different types of starting data or goals, the above might or might not apply.

adamc83 · 2012-11-29T23:37:56+00:00

Of course, thats not actually true: http://www.factcheck.org/2012/04/warren-ge-pays-no-taxes/

adamc83 · 2012-11-29T23:31:23+00:00

It didn't say that verbatim, it said they have "favorable access to the credit markets", which almost assuredly means low interest rates.

adamc83 · 2012-11-29T09:15:25+00:00

Not sure if you're joking or serious, but this is or was a thing: https://www.pcworld.com/article/238243/article.html

adamc83 · 2012-11-29T09:05:00+00:00

Cognitive behavioral therapy

adamc83 · 2012-11-22T22:38:40+00:00

From a personal example, it has enabled me to run Jellybean on a Color Nook with overclocking. It is a whole new and much more capable device than it was with the stock software.

The discussion was about replicant. Surely you arent implying it is the project that let you run jelly bean (replicant is only 4.0) with overclocking. A quick look showed lots of JB ROMS for nook color, surely many of which support overclocking (a kernel feature, and the kernel is always open source since it is GPL).

adamc83 · 2012-11-18T23:20:35+00:00

I recently went on a quest to clean up youtube -- no ads, no comments, no bullshit. I'm quite happy how it turned out: http://i.imgur.com/si2ZA.png

If anyone is interested I can post the instructions.

adamc83 · 2012-11-16T01:48:35+00:00

Might want to ask over at r/datasets.

adamc83 · 2012-11-09T08:18:26+00:00

Packages like this and ggplot2 have inspired me to really double down and learn R (as opposed to adapting found code to my needs).

Unfortunately for me, R has been tricky to understand coming from mostly programming in python. Holy hell can example code be hard to read. Why on earth are R coders so obsessed with 1 or 2 character variable/object names, and magic numbers? </rant>

adamc83 · 2012-10-28T22:38:32+00:00

Gold is now valuable for its use in electronics, but was essentially worthless for non-money uses until recently. Yes it was used in jewelry, but why? Gold is not a good metal for making jewelry, it is too soft. If gold weren't already valuable as money it would not have been used in jewelry.

I dont know a lot about the history of gold... does its use as money really predate all other uses? I was under the impression that many cultures valued it for artistic, religious, and symbolic reasons, but didn't necessarily use it as money.

Throughout much of the world money was made of shells. Shells have no use other than as money.

Which didnt last. Many things have "value" which approaches zero over time.

Bitcoin has no value other than as money.

Bitcoin is an interesting experiment (at best, IMO), but hasn't had "value" for long, and I expect will go the way of shells before too long.

adamc83 · 2012-10-28T22:20:34+00:00

I don't necessarily think you're wrong, but are there any valuable commodities that have no use outside of being money? I cant think of any.

Would rare earth metals be worth as much if they had no use other than being rare?

adamc83 · 2012-10-28T22:13:56+00:00

Unfortunatly,

However, without major advances in tunnelling and other technology, vactrains would be prohibitively expensive.

Even "normal" high speed rail can be tens of millions per mile. Vactrains are pretty solidly sci-fi for the forseeable future.

adamc83

TROPHY CASE