2. FBW 10-11-2011 Wim Van Criekinge

5. Needleman-Wunsch-edu.pl The Score Matrix ---------------- Seq1(j) 1 2 3 4 5 6 7 8 9 10 Seq2 * C K H V F C R V C I (i) * 0 -1 -2 -3 -4 -5 -6 -7 -8 -9 -10 1 C -1 1 0 -1 -2 -3 -4 -5 -6 -7 -8 2 K -2 0 2 1 0 -1 -2 -3 -4 -5 -6 3 K -3 -1 1 1 0 -1 -2 -3 -4 -5 -6 4 C -4 -2 0 0 0 -1 0 -1 -2 -3 -4 5 F -5 -3 -1 -1 -1 1 0 -1 -2 -3 -4 6 C -6 -4 -2 -2 -2 0 2 1 0 -1 -2 7 K -7 -5 -3 -3 -3 -1 1 1 0 -1 -2 8 C -8 -6 -4 -4 -4 -2 0 0 0 1 0 9 V -9 -7 -5 -5 -3 -3 -1 -1 1 0 0 A: matrix(i,j) = matrix(i-1,j-1) + (MIS)MATCH if (substr(seq1, j-1 ,1) eq substr(seq2, i-1 ,1) B: up_score = matrix(i-1,j) + GAP C: left_score = matrix(i,j-1) + GAP a b c

14. FastA (http://www.ebi.ac.uk/fasta33/) Blosum50 default. Lower PAM higher blosum to detect close sequences Higher PAM and lower blosum to detect distant sequences Gap opening penalty -12, -16 by default for fasta with proteins and DNA, respectively Gap extension penalty -2, -4 by default for fasta with proteins and DNA, respectively The larger the word-length the less sensitive, but faster the search will be Max number of scores and alignments is 100

15. FastA Output Database code hyperlinked to the SRS database at EBI Accession number Description Length Initn, init1, opt, z-score calculated during run E score - expectation value, how many hits are expected to be found by chance with such a score while comparing this query to this database. E() does not represent the % similarity

20. BLAST - B asic L ocal A lignment S earch T ool

22. The big red button Do My Job It is dangerous to hide too much of the underlying complexity from the scientists.

29. S Length of extension Score Trim to max indexed * *Two non-overlapping HSP’s on a diagonal within distance A

30. S Length of extension Score Trim to max indexed * *Two non-overlapping HSP’s on a diagonal within distance A

53. Comparing distributions   Extreme Value: Gaussian:

59. -74 -73 -72 * -71 ***** -70 ******* -69 ********** -68 *************** -67 ************************* -66 ************************* -65 ************************************ -64 ***************************************** -63 ************************************************************ -61 ************************ -60 ***************************** -59 ******************* -58 ************** -57 ********* -56 ******** -55 ***** -54 **** -53 * -52 * -51 * -50 -49 Needleman-wunsch-Monte-Carlo.pl (Average around -64 !)

98. PSSM (Position Specific Scoring Matrice)

99. PSSM (Position Specific Scoring Matrice)

100. PSSM (Position Specific Scoring Matrice)

103. From: http://bioweb.pasteur.fr/seqanal/blast/intro-uk.html PSI-BLAST PSSM PSSM

104. PSI-BLAST

105. PSI-BLAST

106. PSI-BLAST

107. PSI-BLAST

111. PHI-Blast Local Blast (Pattern-Hit Initiated BLAST)

112. PHI-Blast Local Blast From: http://bioweb.pasteur.fr/seqanal/blast/intro-uk.html

113. PHI-Blast Local Blast

114. PHI-Blast Local Blast

115. PHI-Blast Local Blast

120. BLAT Human Genome Browser