Abstract:
:We discuss the statistical significance of local similarities found between DNA sequences, and illustrate the procedure with reference to the Queen and Korn algorithm. If the longest similarity found for two sequences has length L, this length is said to be significant at the 5% level if there is a probability of no more than 0.05 of finding a length of L or greater between a pair of sequences consisting of randomly chosen bases with the same overall base frequencies. The distribution of longest lengths is related to that of lengths from any particular pair of starting positions on the two sequences. For our implementation of the Queen and Korn algorithm, this latter distribution is constructed by combining the five different blocks of bases that may be added to extend a similarity. A table is given to assess the significance of longest similarities in sequences of length up to 1000 bases. Quite long similarities are expected to occur by chance alone. The critical values we calculate for assessing significance are preferable to expected numbers of similarities used by some commercial computer packages.
journal_name
Genomicsjournal_title
Genomicsauthors
Brooks LD,Weir BS,Schaffer HEdoi
10.1016/0888-7543(88)90081-xsubject
Has Abstractpub_date
1988-10-01 00:00:00pages
207-16issue
3eissn
0888-7543issn
1089-8646pii
0888-7543(88)90081-Xjournal_volume
3pub_type
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