Primer Blast can be used for comparing short nucleotide sequences to the cpn60 nucleotide database. We are using standard BLAST (blastn) with a word size of 7 (-W 7) and an expect value of 1000 (-e 1000). You can select the number of scores and the number of alignments that you wish to have included in your results file.
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
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Related topics on cpnDB: