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.
References:
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.
For more detailed information, please follow the link(s) below:
http://www.ncbi.nlm.nih.gov/books/NBK21097/
Related topics on cpnDB: