##( mork calling hometown... come in hometown! )##
I just saw your question about block substitution matrices over in the vc++ forum and wanted to make a few comments. However, we should stick to a more appropriate forum. I'd PM you, but its very difficult to use PMs because I easily hit the ceiling and have to break responses into several separates (which begs the question of why there are limits in the first place since I will take up just as much if not more database space because I won't be confined that easily -- same goes for forum posts but at least I don't have to break things up as often).
First I should stress that those kinds of calculations are not really a focus of mine. I've tossed together a few programs before to calculate phylogenetic information from sequences to help me study, but those involved more simplified models than the programs the professionals use regularly. But I'll try to explain what I can.
Laboratories everywhere these days are cranking out gene sequences. There is a whole industry of rather poorly paid lab techs who chop up genomes, gel separate them, run PCRs, and then do various spectral or antibody tests to identify the various fragments. What this results in is a huge collection of DNA sequence information from all sorts of bacteria, plants, fungi, animals, etc. being passed around the scientific and industrial communities. ACCTGTCGATTACA...
One of the useful pieces of information that can be formed from this information is the evolutionary relationships between the various species. The basic theory is that DNA sequences which differ by a lot indicate species which diverged evolutionarily furthur back in history than sequences which are more closely similar.
However, one needs to come up with a good measure for the differences between sequences. One of the simpler possibilities is to just use an extended Hamming distance, where you just count the number of different letters per position in a sequence. However, this is not very useful because one common evolutionary mutation is an insertion event, which will put a new nucleotide or series of nucleotides into a sequence somewhere in the middle of a gene, tossing off all subsequent matches and indicating a large distance between the sequences even though only one evolutionary event occured.
So instead, the similarities are often weighted and a pattern matching algorithm is applied to measure the distances, and often the algorithms are applied to a full codon (3 nucleotides - which collectively code for one amino acid in the gene's protein product). The reason there needs to be a weighting is because another common evolutionary event is substitution, and it has been found that substitutions are more common between amino acids that share similar biochemistries. So experiments have been done, and various substitution theories have been developed. Most often these are represented in scoring matrices, such as the various BLOSUMs. Effectively, each type of scoring matrix describes a particular evolutionary model being applied.
It looks like the question is asking to just basically look up in the matrix the corresponding substitution values between various amino acids with similar properties (for example, V is valine), in order to illustrate to the student that they will have proportionately more likelihood for substitution. I don't have a copy of the BLOSUM50 matrix around, so I couldn't help out much with walking through the problem, but I'm sure its out there on the internet, maybe even on the site your question comes from. But its basically looking things up in a matrix, and not too exciting.
However, as I mention above, this isn't really the field I am most interested in. Particularly recently, I have been much more focused on simulations surrounding the origins of life.
Re: ##( mork calling hometown... come in hometown! )##
Quote:
Originally posted by galathaea
Laboratories everywhere these days are cranking out gene sequences.
Mostly in Maryland thank you very little :D
since the day i have no wonder
First Fiona, I didn't know where to begin to tell you, but I must say that I also find myself confused about some of your posts. But it is ok, lets forget about it.....
Short message for you, if you come back read this: There is always mess that people make up, you shouldn't try to clean them up. Because their making mess is just to put food on their table. It's hard to make a living in reality. You're differerent and you haven't spent day and night to be severely reprimanded by boss so that you can put into your pocket some dollars.
Said many times, but one more time and one more time etc, mightnot ever seem enough...Don't worry, I am not offensive, Because we are human, short of memory...so, I think you might have forgotten !!!
Second, I post right in this thread, so I am sure my evolutionary professor already undestand the main purpose of what I really would like to tell...
I call you professor, I hope you already understand how exactly I am thinking about you...We used to give each other some :) nice words, right ? But there is one thing I would like you to know for sure that Fiona and I have never had any intentions to be impolite to you...Please trust me on that ! And now my coming here to post in your thread is only to stress that one more time...
I don't come to post much because I don't have any problems, all of the solutions to my problems are all around the net, I come here to read and know quite well how everything is going on.
As far as I know, Humanity had evolved three distincly different brain circuits for mating and reproduction. One circuit is for the sex drive, the second one is for romantic love and the last one is attachment, that sense of calm that you can feel with a long-term partner. All of these have close relations to each other.
Scientifically, women love words, and Words are also women's tool. When a woman hears some words from the one she loves, she would have a feeling of the romantic passion, which is a very important point and that also tells us that some parts of the brain that have relations to such feelings are being in an active state. It is not only for love words but for any other stimuli like getting mad, getting excited etc...you can still have the same conclusion.
However, everyone I think should know that itis not as much the words as it is all the activity that goes with the words, and since women love words, this can become a real target for sex cybers that hiding everywhere on the net with different names, like mutiagents in a unique system evironment...it is different from people to people, but the main purpose is to satisfied themselves, they don't have to pay for anything but still able to reach the climax.
As far as I have observed, their words become more, and their actions get more and more active, and you know, they becomes more than or over a normal level whenever those people have any clues about any possibilities to suck their targets in, even though such clues are just a few, some. But what is exactly in their words ? I think it also changes much between people. When you hear "I love you" without any inflection, in most of situations, it will be hard for you to have any romantic passion than the one with some kind of inflection, right?.
But how can people use inflections in such three boring words? I don't know, but I can say those words are boring and the fact is that there are not many couples who will give each other such words, This is why I think another way of communication comes into existence, it is non-verbal. I didn't mean people with so many words are liars, but their words are easily recognized as true or false when you turn yourself into them, under what situations they would say this, under what circumstances they would say that and many many more.....
I don't focus on any pictures before me, because the transition from cut-to-fit craftmanship to the automated mass-production of goods from interchangeable parts already took about 200 year, it went from the interchangeable parts, to assembly lines then to automated assembly lines, things now develop more and more each day, those pictures are now just for present_ness, for now_ness, not for future_ness.
I know there is one kind of pain for which nobody has yet found a cure-the pain of that comes from the ending of a relationship. It could be anything, marriage, love affair, deep friendship; in fact any strong emotional tie between the two people.
Yes, it is true that no cure has been found but people who have gone through this kind of broken relationship all agree that time is the great healer. How much time will vary from person to person, but it is 80% true that grief will last as long as the original relationship lasted. The sad thing all people have to admit is that when the breakdown occurs, we can only stumble forward over the stones beneath our feet, it is all dark ahead and we will fall painfully many many times before we begin to see the light at the end of the tunnel...
In all, there is NEVER ever ONE solution to any problems, it is just taking a few minutes, a few days, a few months or let it be a few years for one to find another truly BETTER solution, no one knows when it comes, but it surely comes !!!
Being stronger and more detemined, more consistent, especially MORE CONFIDENT is the most prerequisitte to get over all the obstacles ahead...At least I take it for granted...
