A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments
نویسندگان
چکیده
We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature.
منابع مشابه
Score distributions of gapped multiple sequence alignments down to the low-probability tail.
Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are exponentially small. For gapless local alignments of infinitely long sequences this distribution ...
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Background: The optimal score for ungapped local alignments of infinitely long random sequences is known to follow a Gumbel extreme value distribution. Less is known about the important case, where gaps are allowed. For this case, the distribution is only known empirically in the highprobability region, which is biologically less relevant. Results: We provide a method to obtain numerically the ...
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ورودعنوان ژورنال:
- International journal of bioinformatics research and applications
دوره 10 2 شماره
صفحات -
تاریخ انتشار 2014