Align

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)