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Pages 65-69

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From page 65... ... The design of scoring schemes that properly weigh alignments to expose biologically meariingfi~1 local similarities is the subject of much investigation. The score of alignments between protein sequences is the sum of scores assigned to individual pairs of aligned symbols, just as for Read the entire page →
From page 66... ... The basic issue in local alignment, just as in the case of global alignment, is to find a path of maximal score. However, there are more degrees of freedom in the local alignment problem: where the paths begin and where they end is not given a priori but is part of the problem. Read the entire page →
From page 67... ... v: 1 ~1 z ~1 ~ l ~ l l x l l ~ l o cy lv l l l c l c l l l ~ - l l ~ l l o l l l l l l l l ~ ~ ~ I ~ I I I I I t I I I ~ ~ ~ ~ ~ _ ~ oo oo ~ ~ oo ~ ~ ~ ~ ~ 1 1 1 1 1 1 1 1 1 1 1 1 1 oo ~ ~ o ~ ~ ~ ~ _ ~ o ~ ~ ~ 1 1 1 1 1 1 1 1 1 1 1 I ~ I ~ o I I ~ _ ~ ~ ~ _ oo _ _ ~ I I o o o _ ~ ~ ~ I ~ ~ ~ _ ~ o t ~ o t t I I I t I I ~ t ~ t t ~ ~ I -c t I t ~ t I I t t � 0 1 1 1 ~ t t I I t I I I I I t I t _ 0 _ I ~ ~ I ~ t I I ~ I I I t I I ~ ~ I ~ ~ 0 0 1 _ ~ c~ I 0 I I t I t I I 0 0 1 1 0 _ ~ _ oo oo oo oo oo oo oo oo oo oc 1 1 1 1 1 1 1 1 1 1 I I I 0 1 1 ~ ~ I I I I oo _ t I ~ ~ I I 0 I ~ ~ ~ ~ I I I ~ _ _ ~ ~ ~ t I I ~ ~> c~ ~ r~ t ~ ~ ~ ~ ~ w~ < t � I t I I I ~ I 1 0 1 1 ~ _ ~ ~ ~ _ - , 1 1 1 1 1 1 I ~ I I I I t I o I I o I I I I I ~ ~ ~ ~ ~ ~ ~ ~ oo ~ ~ 1 1 1 1 1 1 1 1 1 1 I I t I I � t I t I ~ � t I t I I I I I I ~ I t -- -~ t � ~ oo oo oo ~ oo ~ ~ ~ oo 1 1 1 1 1 1 1 1 1 1 � ~ Z ~ ~ ) Read the entire page →
From page 68... ... At this level of resolution, the small gaps in the alignments of the second and third segment pairs appear as small discontinuities in paths that otherwise follow the direction of the diagonal of the edit graph and or matrix. When the sequences become very large, say on the order of 100,000 nucleotides, then small local alignments are not seen, and neither are gaps in large alignments unless they are very large. Read the entire page →
From page 69... ... Lo v v ~ En V ED H En ~ A H H VV be; ~ a ~ U) Read the entire page →

From page 65...

... The design of scoring schemes that properly weigh alignments to expose biologically meariingfi~1 local similarities is the subject of much investigation. The score of alignments between protein sequences is the sum of scores assigned to individual pairs of aligned symbols, just as for

Read the entire page →

From page 66...

... The basic issue in local alignment, just as in the case of global alignment, is to find a path of maximal score. However, there are more degrees of freedom in the local alignment problem: where the paths begin and where they end is not given a priori but is part of the problem.

Read the entire page →

From page 67...

... v: 1 ~1 z ~1 ~ l ~ l l x l l ~ l o cy lv l l l c l c l l l ~ - l l ~ l l o l l l l l l l l ~ ~ ~ I ~ I I I I I t I I I ~ ~ ~ ~ ~ _ ~ oo oo ~ ~ oo ~ ~ ~ ~ ~ 1 1 1 1 1 1 1 1 1 1 1 1 1 oo ~ ~ o ~ ~ ~ ~ _ ~ o ~ ~ ~ 1 1 1 1 1 1 1 1 1 1 1 I ~ I ~ o I I ~ _ ~ ~ ~ _ oo _ _ ~ I I o o o _ ~ ~ ~ I ~ ~ ~ _ ~ o t ~ o t t I I I t I I ~ t ~ t t ~ ~ I -c t I t ~ t I I t t � 0 1 1 1 ~ t t I I t I I I I I t I t _ 0 _ I ~ ~ I ~ t I I ~ I I I t I I ~ ~ I ~ ~ 0 0 1 _ ~ c~ I 0 I I t I t I I 0 0 1 1 0 _ ~ _ oo oo oo oo oo oo oo oo oo oc 1 1 1 1 1 1 1 1 1 1 I I I 0 1 1 ~ ~ I I I I oo _ t I ~ ~ I I 0 I ~ ~ ~ ~ I I I ~ _ _ ~ ~ ~ t I I ~ ~> c~ ~ r~ t ~ ~ ~ ~ ~ w~ < t � I t I I I ~ I 1 0 1 1 ~ _ ~ ~ ~ _ - , 1 1 1 1 1 1 I ~ I I I I t I o I I o I I I I I ~ ~ ~ ~ ~ ~ ~ ~ oo ~ ~ 1 1 1 1 1 1 1 1 1 1 I I t I I � t I t I ~ � t I t I I I I I I ~ I t -- -~ t � ~ oo oo oo ~ oo ~ ~ ~ oo 1 1 1 1 1 1 1 1 1 1 � ~ Z ~ ~ )

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From page 68...

... At this level of resolution, the small gaps in the alignments of the second and third segment pairs appear as small discontinuities in paths that otherwise follow the direction of the diagonal of the edit graph and or matrix. When the sequences become very large, say on the order of 100,000 nucleotides, then small local alignments are not seen, and neither are gaps in large alignments unless they are very large.

Read the entire page →

From page 69...

... Lo v v ~ En V ED H En ~ A H H VV be; ~ a ~ U)

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