One of the most common activities in bioinformatics is the search for similar sequences. These searches are usually carried out with the help of programs from the NCBI BLAST family. As the majority of searches are routinely performed with default parameters, a question that should be addressed is how reliable the results obtained using the default parameter values are, i.e. what fraction of potential matches have been retrieved by these searches. Our primary focus is on the initial hit parameter, also known as the seed or word, used by the NCBI BLASTn, MegaBLAST and other similar programs in searches for similar nucleotide sequences. We show that the use of default values for the initial hit parameter can have a big negative impact on the proportion of potentially similar sequences that are retrieved. We also show how the hit probability of different seeds varies with the minimum length and similarity of sequences desired to be retrieved and describe methods that help in determining appropriate seeds. The experimental results described in this paper illustrate situations in which these methods are most applicable and also show the relationship between the various BLAST parameters.
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