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iHMMune-align Model Probabilities FileThe probabilities associated with different aspects of the HMM are stored within the 'Model Probability File'. This file contains the data for N-addiiton to both the IGHV-IGHD (N1) and IGHD-IGHJ (N2) regions, along with exonuclease data for the region ends. N-addition data is given as probabilities for adding another N nucleotide after the current addition. For example, the first value ([0]) represent the probability of having a single N addition, the second value ([1]) is the probability of adding a second nucleotide to the N-REGION and so on up to 40 N-additions ([39]).Exonuclease data is provided on a per family basis for the IGHV end, both the 5` and 3` IGHD ends and the start of the IGHJ. The data is given as mean number of removals from a gene end, along with a standard deviation. These are used to calculate the probabilities for exonuclase removals from the gene segement ends using a normal distribution with the means and standard deviations specified. An example of the 'Model Probability File' is provided below. It is important that the format be retained for any custom files. This is best achieved by cutting and pasting this example file to a text editor and changing the required values. VD_N and DJ_N are the N1 and N2 addition probabilities. The *_exo_mean and *_exo_stdDev are the mean and standard deviations for the exonuclease removals from the gene ends. [Note: the P related data are deprecated and are temporarily retained but set to 0] |
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