Algorithms on Sequences

Recent Blasts
• Blast2 (Gapped Blast,1997) : version of Blast with indels,
filtering Dust and Seg and threads for multi-processors.
• PSI-Blast (Position Specific Iterated Blast) : iterative
version of Blast in view of phylogeny studies, where the comparison
matrix used at one step takes into account consensus found at the
previous step, for a multiple alignment of sequences with a sufficient
E-value, until the processus has converged.
• PHI-Blast (Pattern-Hit Initiated Blast) : fast version of
Blast, that may be combined with PSI-Blast, where one gives a
pattern (regular expression Prosite-like) that must be used in the
alignment of sequences)
Dotplots :
The simplest way to see alignments
Dotplot = identity matrix of two sequences
Similarities =
diagonals
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Filtering, Smoothing
(window 4, 1 error)
DNA /cDNA of actin gene from
muscle of Pisaster ochraceus
(horizontal / vertical)