Difference between revisions of "Tutorial"
From victor
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* Profile to profile | * Profile to profile | ||
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| + | Alignment algorithm: | ||
* Local | * Local | ||
* Global | * Global | ||
* Freeshift | * Freeshift | ||
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| + | Blosum substitution matrix: | ||
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| + | #62 | ||
| + | #45 | ||
| + | #50 | ||
| + | #80 | ||
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Weighting scheme (only for profiles): | Weighting scheme (only for profiles): | ||
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* Henikoff (Henikoff & Henikoff, 1994) | * Henikoff (Henikoff & Henikoff, 1994) | ||
* SecDivergence (Rychlewski et al., 2000) | * SecDivergence (Rychlewski et al., 2000) | ||
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Scoring function (only for profile to profile alignments): | Scoring function (only for profile to profile alignments): | ||
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** AtchleyCorrelation | ** AtchleyCorrelation | ||
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Revision as of 13:48, 19 August 2014
Target/Template alignment
Supposing you have already found a good template, now 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
- Dot product
- DotPFreq
- DotPOdds
- EDistance (Euclidean distance)
- Pearson
- JensenShannon
- Atchley metric
- AtchleyDistance
- AtchleyCorrelation
The fist step is to put the target and the template fasta sequences in a single file like that:
>target VLEEIAKDHGEALTI.... >template AFQVTSIPTLILFQ....
For more detail use the option -h with the subali application or see the AlignTest code.
