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User: Tjunier

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Contents

1 Features of Japanese Blades

2 Sequence Alignments

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Features of Japanese Blades

Note. Obviously some pictures would be useful. If I can't find non-copyrighted material somewhere, I might try a drawing or two. Meanwhile please see the websites mentioned in the references, as they have excellent images.

Type of blade

Parts of the blade

These features are not present on all blade types; for example some blades don't have a yokote, etc.

Curvature (Sori)

Cross-section (Sugata)


References

Books

External links


Sequence Alignments

Quality measure

To find a "good" alignment, we need to have a way of assessing the quality of an alignment. This is done by a scoring scheme. The scheme assigns a score to all positions in the alignment, and the alignment score is the sum of all position scores. The simplest scores assign 1 to matches and -1 to mismatches and gaps (there are other, more complicated schemes). Under such a scheme, the following alignment

att-cccag
||| || ||
attgcctag

has a score of 5 (7 matches, 1 mismatch, 1 gap).

It should be noted that in some cases the best possible score isn't achieved by a single alignment, but by many ones. As a trivial example, consider the sequences c and ccc, the highest score (under the same scheme as above) is exhibited by the three alignments

c--   -c-   --c
|      |      |
ccc   ccc   ccc

Finding the best one(s)

Alignments as Paths

Alignments can be represented as "paths" in a graph. If we represent the two sequences at the sides of a lattice of squares, an alignment is a path through the lattice that starts at some node only "moves" down, right, or both (diagonally). Exactly where it starts and ends depends on the kind of alignment.

For example using the same two sequences as above, attcccag and attgcctag, we may represent the lattice as a table [gotta find something esle than HTML tables for this]:

attgcctag
a\
t\
t\
c-\
c\
c\
a\
g\


There are many ways [some stuff about the exact number here] of aligning two sequences. In fact, there are so many that brute force is out of the question. The most commonly used approach is dynamic programming.


Wasp article

Howdy, I just edited Wasp and found that the I did not register as a user in the page history - am at a public library right now, no cookies?. Please take a look at the opening, am most interested in a read of that first sentence (seems clearer to me this way). I found three useful references prior to making the division changes, will post them next session. --azwaldo 02:55, 7 Jan 2004 (UTC)

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Last Contributor: Tjunier - Article Talk Page: Discussion - GNU FDL: Verbatim Source

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