Align
From victor
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)