Subsequences that differ by one in the number of defined bases are also compared to each other using a threshold to correct for the higher expected count of the subsequence that contains lower number of defined bases.
The flanking vector sequences were removed; the sequences trimmed to areas of high chromatograph quality and ambiguously defined bases corrected.
In this method, a subsequence is aligned to all other subsequences, and its count is compared to counts of subsequences that contain n − 1 perfectly matching bases, where n is the maximum number of defined bases in the aligned subsequences.
Formally, Huddinge distance between two gapped or ungapped subsequences is defined as d − a, where d is the maximum number of defined bases in either of the compared subsequences, and a is the maximum number of bases that can be perfectly aligned between them without introduction of new gaps.
(A, B ) A four base ungapped subsequence 'ACGT' and types of subsequences that are at Huddinge distance of one from it (A ) and a gapped subsequence with four defined bases 'ACnGT' and types of subsequences that are at Huddinge distance of one from it (B ).
Comparison of subsequences with different number of defined bases (shorter, longer and shorter with gap) requires a threshold to compensate for the fact that shorter subsequences that match perfectly to longer ones are always present at equal or higher numbers than the longer subsequence.
