The descriptions that I've found say it's the log odds ratio (observed/expected) where expected is the assumption that there is no correlation between amino acids.  I'm slightly confused as to what this means? Do we have a database of sequences and if there are 10 A's out of 1000 amino acids is it's expected simply 10/1000 * sequence length for all sequences?   What is the observed? Is the observed different for every sequence so there is a different BLOSUM matrix for each sequence? And can someone explain how this table represents 62% of "kept identity"?   Sorry if these questions seem nonsensical or vague, I'm not of a biology background.
The  states that:      The scores are created by comparing the word in the list in step 2* with all the 3-letter words. By using the scoring matrix (substitution matrix) to score the comparison of each residue pair, there are 203 possible match scores for a 3-letter word. For example, the score obtained by comparing PQG with PEG and PQA is 15 and 12, respectively with the BLOSUM62 weighting scheme.   I do not understand how they got a score of 15 for PQG v. PEG. What is a scoring matrix, how is it computed, and how is it used?      Step 2 on that page is Make a k-letter word list of the query sequence: “Take k=3 for example, we list the words of length 3 in the query protein sequence (k is usually 11 for a DNA sequence) sequentially, until the last letter of the query sequence is included”.
So, let's take Skeptics.SE for an example. You can become a trusted user when you acquire 4000 rep., not 20000  I was like, wow, so is it like this because of the lack of users on Skeptics.Se, as in, not so much as Stack Overflow or something?  Why do some sites need less reputation to be a trusted user? I was recently told (  ):     You cannot delete a class in production directly. You will need delete   the class from your sandbox and then deploy the deletions to your   production org.   When you deploy from sandbox to production, the   missing classes will come up in red and you can choose to deploy these   deletions to Production.   However, I'd like some clarification because finding information on how to do this is like pulling teeth, unfortunately.  Am I supposed to:   Delete the Trigger in Sandbox Make a deployment package in Sandbox Add the Trigger which is going to be listed in RED now Deploy (and that deletes it from Production)?   I am not seeing deleted Triggers in Red in Sandbox.  Are they NOT listed under "Triggers" for deployment, but elsewhere?   Frustrated = true.   Does this ONLY apply to Classes??  UPDATE:  I just tried again, with a CLASS, and it still doesn't show up at all as a Deployable package (red or not) after I delete it in the Sandbox.  UPDATE 2:  I was just able to delete a class, that I know was written via IDE from a third party, in both Sandbox and Production.  So now I'm wondering if it has to do with where it was originally deployed from (if from IDE, IDE can delete it - it from Sandbox, you have to jump through hoops).  :-( Is adding a time dummy the same as estimating by within-time fixed effects? Can you Start Skyrim 'silent' without the launcher showing up? Recommended way to initialize srand? I need a 'good' way to initialize the pseudo-random number generator in C++. I've found  that states:     In order to generate random-like   numbers, srand is usually initialized   to some distinctive value, like those   related with the execution time. For   example, the value returned by the   function time (declared in header   ctime) is different each second, which   is distinctive enough for most   randoming needs.   Unixtime isn't distinctive enough for my application. What's a better way to initialize this? Bonus points if it's portable, but the code will primarily be running on Linux hosts.  I was thinking of doing some pid/unixtime math to get an int, or possibly reading data from /dev/urandom.  Thanks!  EDIT  Yes, I am actually starting my application multiple times a second and I've run into collisions. It is common for public Wi-Fi access points to include login pages, even at times, when they’re free (i.e. Starbucks, many airports, hotels, etc).  I’m often in a situation where I’ll open up Chrome/Firefox, with and all my previously open tabs will start to reload.  If there is a wireless login redirection page, however, every tab is redirected and reloaded and the previous page is lost from history (and the back button won't return to it).  Is there any way to avoid or circumvent this behavior? Attribute editing in QGIS on geoJson file We have vector files in the format of geoJson files. We need to keep it in geoJson format as it is picked up by mobile devices via Restful services.  The problem is we want to change the attributes of the features in QGIS but it seems like this is not possible. We don't have to add or remove columns. We simply need to edit the existing data.  Is there a work around for this?  Are there any plugins that I can download that will allow me to do this in QGIS? Word for person always after what he does not have and not cherishing what he has Possible Duplicate:          Is there a word for a person who is always after what he does not have and does not cherish what he has? If not, any idiom or phrase? How do I inspect the view hierarchy in iOS? Should I keep my swap file on an SSD drive? I'm considering getting an SSD drive to run as the primary OS partition.  As I understand, this should provide a substantial improvement in performance.     My question is this: Should I leave the swap file on that drive?     The swap partition will be largely random seeks and so should benefit from the speed.  On the other hand, it will be constantly written to which will wear out the drive faster. Is Ubuntu based on Debian unstable or Debian testing? which of the two it is? $K/F$ is a field extension of finite degree $n$. How can I prove that $K$ is isomorphic to a subfield of the ring of $n\times n$ matrices over $F$, so the ring of $n\times n$ matrix over $F$ contains an isomorphic copy of every extension of $F$ of degree $\leq n$? Finding a 2x2 Matrix raised to the power of 1000 Remove "Show Desktop" button next to the clock in Windows 7 Get selected element's outer HTML What is economics like for ordinary people in the Star Trek universe? Can apostrophe 's' be used with 'etc.'? Using \@-ified punctuation while using \frenchspacing After reading  about spacing and punctuation, I was left wondering about an issue that didn't seem to be addressed: using \frenchspacing together with the modified punctuation \@., \@?, etc.  As far as I can tell visually, using \frenchspacing together with these commands works correctly (i.e., it seems like nothing breaks, and the extra space is suppressed as normal), but are there problems that can arise from doing so?   Moreover, when using \frenchspacing, "should" I still use \@. and its friends where it would ordinarily be necessary, in case someone wants to remove \frenchspacing later? Would accommodating (hypothetical) future editors in this way be "standard", "above and beyond the call of duty", or "crazy"? Crash with error "No more room to grow table" How to evaluate these two integrals.