Difference between revisions of "Align"

From victor
Jump to: navigation, search
(Created page with " Supposing you have already found a template candidate, you need to align it against your target sequence. The '''subali''' application let you choose from very different typ...")
(No difference)

Revision as of 13:57, 19 August 2014

Supposing you have already found a template candidate, you need to align it against your target sequence. The subali application let you choose from very different type of algorithms, strategies and parameters.

Strategy:

  • Sequence to sequence
  • Profile to sequence
  • Profile to profile


Alignment algorithm:

  • Local
  • Global
  • Freeshift


Blosum substitution matrix:

  • 62
  • 45
  • 50
  • 80


Weighting scheme (only for profiles):

  • PSIC (Sunyaev et al., 1999)
  • Henikoff (Henikoff & Henikoff, 1994)
  • SecDivergence (Rychlewski et al., 2000)


Scoring function (only for profile to profile alignments):

  • Sum of pairs
    • CrossProduct
    • LogAverage (Ohsen and Zimmer, 2003; von Ohsen et al., 2003)
  • Dot product
    • DotPFreq (Wang and Dunbrack, 2004)
    • DotPOdds (Wang and Dunbrack, 2004)
  • EDistance (Euclidean distance)
  • Pearson (Pietrokovski, 1996)
  • JensenShannon (Yona and Levitt, 2002)
  • Atchley metric
    • AtchleyDistance (Atchley et al., 2005)
    • AtchleyCorrelation (Atchley et al., 2005)