Bioinformatic tools have become essential to biologists in their quest to understand the vast quantities of sequence data, and now whole genomes, which are being produced at an ever increasing rate. Much of these sequence data are single-pass sequences, such as sample sequences from organisms closely related to other organisms of interest which have already been sequenced, or cDNAs or expressed sequence tags (ESTs). These single-pass sequences often contain errors, including frameshifts, which complicate the identification of homologues, especially at the protein level. Therefore, sequence searches with this type of data are often performed at the nucleotide level. The most commonly used sequence search algorithms for the identification of homologues are Washington University’s and the National Center for Biotechnology Information’s (NCBI) versions of the BLAST suites of tools, which are to be found on websites all over the world. The work reported here examines the use of these tools for comparing sample sequence datasets to a known genome. It shows that care must be taken when choosing the parameters to use with the BLAST algorithms. NCBI’s version of gapped BLASTn gives much shorter, and sometimes different, top alignments to those found using Washington University’s version of BLASTn (which also allows for gaps), when both are used with their default parameters. Most of the differences in performance were found to be due to the choices of default parameters rather than underlying differences between the two algorithms. Washington University’s version, used with defaults, compares very favourably with the results obtained using the accurate but computationally intensive Smith–Waterman algorithm.