Tutorial

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Target/Template alignment

To initiate the alignment process you need to put the target and the template fasta sequences in a file, that will be the input file for the application.

>target
VLEEIAKDHGEALTI....
>template
AFQVTSIPTLILFQ....

Then depending of what type of alignment you want, you can choose between

sequence to sequence
profile to sequence
profile to profile

Also you can choose between the alignment algorithm to use

local
global
freeshift

if you choose profile to sequence or profile to profile type you can decide to use a specific Weighting scheme

PSIC
Henikoff
SecDivergence

And also choose a scoring function

CrossProduct 
LogAverage 
DotPFreq 
DotPOdds 
EDistance 
Pearson 
JensenShannon 
AtchleyDistance 
AtchleyCorrelation 

With all the alignment types you can decide to use a blosum substitution matrix of 62, 45, 50 or 80.

For more detail use the option -h with the subali application or see the AlignTest code.

Build loops

Evaluate a model