Difference between revisions of "Lecture 16"
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| + | This page has not been revised yet for the 2007 Fall term. Some of the slides may be reused, but please consider the page as a whole out of date as long as this warning appears here. | ||
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__NOTOC__ | __NOTOC__ | ||
<small>[[Lecture_15|(Previous lecture)]] ... [[Lecture_17|(Next lecture)]]</small> | <small>[[Lecture_15|(Previous lecture)]] ... [[Lecture_17|(Next lecture)]]</small> | ||
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======Slide 011====== | ======Slide 011====== | ||
[[Image:L16_s011.jpg|frame|none|Lecture 16, Slide 011<br> | [[Image:L16_s011.jpg|frame|none|Lecture 16, Slide 011<br> | ||
| + | (*) Computing E-values is possible for HSPs since the statistcs of gap-less alignments are analytically tractable. Similar conclusions in general cannot be drawn from gapped alignments. Note the E-values are not a statement about the retrieved hit, but a statement about an expected distribution of scores. Or, to rephrase this, a poor e-value does not mean that your hit is not a homologue, but it means that at that score an irrelevant sequence has a a high chance of scoring well due to chance similarities. | ||
| + | ]] | ||
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======Slide 012====== | ======Slide 012====== | ||
[[Image:L16_s012.jpg|frame|none|Lecture 16, Slide 012<br> | [[Image:L16_s012.jpg|frame|none|Lecture 16, Slide 012<br> | ||
| + | (*) Note that restricting by organism is not a restriction on the search, but a restriction on the list of results that are being reported. The search takes just as long. Many databases of model-organism genome projects offer BLAST searches on their specific data. These may be faster. | ||
| + | ]] | ||
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======Slide 013====== | ======Slide 013====== | ||
[[Image:L16_s013.jpg|frame|none|Lecture 16, Slide 013<br> | [[Image:L16_s013.jpg|frame|none|Lecture 16, Slide 013<br> | ||
| + | (*) How many? That depends. Unknown genes (or "ORFans") may comprise a significant (albeit diminishing) fraction of genomes. See [http://linkinghub.elsevier.com/retrieve/pii/S0969212602009383 Siew&Fischer(2003)] and [http://www.cs.bgu.ac.il/~nomsiew/ORFans/ the ORFan database] | ||
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======Slide 014====== | ======Slide 014====== | ||
[[Image:L16_s014.jpg|frame|none|Lecture 16, Slide 014<br> | [[Image:L16_s014.jpg|frame|none|Lecture 16, Slide 014<br> | ||
Latest revision as of 15:28, 1 September 2007
Update Warning! This page has not been revised yet for the 2007 Fall term. Some of the slides may be reused, but please consider the page as a whole out of date as long as this warning appears here.
(Previous lecture) ... (Next lecture)
Fast Sequence Database Searches (BLAST)
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Add:
- Summary points
- Exercises
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Lecture Slides
Slide 001
Lecture 16, Slide 001
Slide 002
Lecture 16, Slide 002
Slide 003
Lecture 16, Slide 003
Slide 004
Lecture 16, Slide 004
Slide 005
Lecture 16, Slide 005
Slide 006
Lecture 16, Slide 006
Slide 007
Lecture 16, Slide 007
Slide 008
Lecture 16, Slide 008
Slide 009
Lecture 16, Slide 009
Slide 010
Lecture 16, Slide 010
Slide 011
Lecture 16, Slide 011
(*) Computing E-values is possible for HSPs since the statistcs of gap-less alignments are analytically tractable. Similar conclusions in general cannot be drawn from gapped alignments. Note the E-values are not a statement about the retrieved hit, but a statement about an expected distribution of scores. Or, to rephrase this, a poor e-value does not mean that your hit is not a homologue, but it means that at that score an irrelevant sequence has a a high chance of scoring well due to chance similarities.
(*) Computing E-values is possible for HSPs since the statistcs of gap-less alignments are analytically tractable. Similar conclusions in general cannot be drawn from gapped alignments. Note the E-values are not a statement about the retrieved hit, but a statement about an expected distribution of scores. Or, to rephrase this, a poor e-value does not mean that your hit is not a homologue, but it means that at that score an irrelevant sequence has a a high chance of scoring well due to chance similarities.
Slide 012
Lecture 16, Slide 012
(*) Note that restricting by organism is not a restriction on the search, but a restriction on the list of results that are being reported. The search takes just as long. Many databases of model-organism genome projects offer BLAST searches on their specific data. These may be faster.
(*) Note that restricting by organism is not a restriction on the search, but a restriction on the list of results that are being reported. The search takes just as long. Many databases of model-organism genome projects offer BLAST searches on their specific data. These may be faster.
Slide 013
Lecture 16, Slide 013
(*) How many? That depends. Unknown genes (or "ORFans") may comprise a significant (albeit diminishing) fraction of genomes. See Siew&Fischer(2003) and the ORFan database
(*) How many? That depends. Unknown genes (or "ORFans") may comprise a significant (albeit diminishing) fraction of genomes. See Siew&Fischer(2003) and the ORFan database
Slide 014
Lecture 16, Slide 014
Slide 015
Lecture 16, Slide 015
Slide 016
Lecture 16, Slide 016
Slide 017
Lecture 16, Slide 017
Slide 018
Lecture 16, Slide 018
Slide 019
Lecture 16, Slide 019
Slide 020
Lecture 16, Slide 020
Slide 021
Lecture 16, Slide 021
Slide 022
Lecture 16, Slide 022
Slide 023
Lecture 16, Slide 023
Slide 024
Lecture 16, Slide 024
Slide 025
Lecture 16, Slide 025
Slide 026
Lecture 16, Slide 026
Slide 027
Lecture 16, Slide 027
Slide 028
Lecture 16, Slide 028
Slide 029
Lecture 16, Slide 029
Slide 030
Lecture 16, Slide 030
