View source for Algorithms in Sequence Analysis 2011-2012

== Schedule==
[[Media:ASA_2011_schedule.pdf | ASA_2011_schedule.pdf]]


== Assignments ==

* [[Algorithms in Sequence Analysis - Assignment 1|Assignment 1]]
* [[Algorithms in Sequence Analysis - Assignment 2|Assignment 2 HMMs]]

==Lectures==

{|
|-
!Lecture Topic   !! Slides   !! Handouts   !! Reading
|-
|Lecture 1 - Pairwise Alignment I
|[[Media:ASA_2011_lec1.pdf | ASA_2011_lec1.pdf]]
|[[Media:ASA_2011_lec1_handout.pdf | ASA_2011_lec1_handout.pdf]]
|
|-
|Lecture 2 - Pairwise Alignment II
|[[Media:ASA_2011_lec2.pdf | ASA_2011_lec2.pdf]]
|[[Media:ASA_2011_lec2_handout.pdf | ASA_2011_lec2_handout.pdf]]
|-
|Lecture 3 - Substitution matrices
|[[Media:ASA_2011_lec3.pdf | ASA_2011_lec3.pdf]]
|[[Media:ASA_2011_lec3_handout.pdf | ASA_2011_lec3_handout.pdf]]
|-
|Lecture 4 - Multiple Sequence Alignment I
|[[Media:ASA_2011_lec4.pdf | ASA_2011_lec4.pdf]]
|[[Media:ASA_2011_lec4_handout.pdf | ASA_2011_lec4_handout.pdf]]
|-
|Lecture 5 - Multiple Sequence Alignment II
|[[Media:ASA_2011_lec5.pdf | ASA_2011_lec5.pdf]]
|[[Media:ASA_2011_lec5_handout.pdf | ASA_2011_lec5_handout.pdf]]
|
|-
|Lecture 6 - Markov models
|[[Media:ASA_2011_lec6.pdf | ASA_2011_lec6.pdf]]
|[[Media:ASA_2011_lec6_handout.pdf | ASA_2011_lec6_handout.pdf]]
|
|-
|Lecture 7 - Hidden Markov Models
|[[Media:ASA_2011_lec7.pdf | ASA_2011_lec7.pdf]]
|[[Media:ASA_2011_lec7_handout.pdf | ASA_2011_lec7_handout.pdf]]
|[[Media:Rabiner.pdf | Rabiner.pdf]]
|[[Media:Krogh.pdf | Krogh.pdf]]
|-
|Lecture 8 - Homology searching I
|[[Media:ASA_2011_lec8.pdf | ASA_2011_lec8.pdf]]
|[[Media:ASA_2011_lec8_handout.pdf | ASA_2011_lec8_handout.pdf]]
|-
|Lecture 9 - Homology searching II
|[[Media:ASA_2011_lec9.pdf | ASA_2011_lec9.pdf]]
|[[Media:ASA_2011_lec9_handout.pdf | ASA_2011_lec9_handout.pdf]]
|-
|Lecture 10 - Evolution/Phylogeny I
|[[Media:ASA_2011_lec10.pdf | ASA_2011_lec10.pdf]]
|[[Media:ASA_2011_lec10_handout.pdf | ASA_2011_lec10_handout.pdf]]
|
|-
|Lecture 11 - Phylogeny II / Sequence motifs I
|[[Media:ASA_2011_lec11.pdf | ASA_2011_lec11.pdf]]
|[[Media:ASA_2011_lec11_handout.pdf | ASA_2011_lec11_handout.pdf]]
|
|-
|Lecture 12 - Sequence Entropy
|[[Media:ASA_2011_lec12.pdf | ASA_2011_lec12.pdf]]
|[[Media:ASA_2011_lec12_handout.pdf | ASA_2011_lec12_handout.pdf]]
|
|-
|Lecture 13 - Sequence motifs II
|[[Media:ASA_2011_lec13.pdf | ASA_2011_lec13.pdf]]
|[[Media:ASA_2011_lec13_handout.pdf | ASA_2011_lec13_handout.pdf]]
|
|-
|Lecture 14 - Genome Analysis / Comparative Genomics 
|[[Media:ASA_2011_lec14.pdf | ASA_2011_lec14.pdf]]
|[[Media:ASA_2011_lec14_handout.pdf | ASA_2011_lec14_handout.pdf]]
|
|-
|}

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