Difference between revisions of "Align"

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(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...")
 
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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)
 

Latest revision as of 14:02, 19 August 2014