Condition Soft filtering with SW Soft filtering no SW Hard filtering with SW Hard filtering with no SW -F "m S" -s T -F "m S" -s F -F T -s T -F T -s F BMC Genomics 2009, 10:490 http://www.biomedcentral.com/1471-2164/10/490 Table 1: The effect of BLAST filtering options on the performance of RBH BLAST options Number of RBHs Normalized value 6773 6779 6570 6507 1.04 1.04 1.01 1 This table shows the performance of RBH using the different BLAST filtering options with eukaryotic sequences. The results from this analysis showed the soft filtering option with no Smith and Waterman produced the highest number of successful RBHs. ure 2 shows a bar chart of the successful RBH results nor- malised to the default BLAST options (-F T, -s F). Contrary to the findings of Moreno-Hagelsieb and Lat- imer 2008 [29], who showed the SW algorithm improved results by 10%, in this study using SW produced 0.0004% (6) less successful results. However the analyses in this work were slightly different to that of Moreno-Hagelsieb and Latimer and are listed here: 1) They used complete bacterial genomes: A) These sequences are generated from genomic DNA and are sequenced in both strands. B) The Carp sequences are gen- erated from single pass (one strand) cDNA sequencing from RNA and, as such, are likely to contain more errors. 2) The protein sequences used in assessing RBH success: A) Moreno-Hagelsieb and Latimer used full length and defined proteins from complete bacterial genomes. B) The carp sequences were partial proteins from 6 frame nucle- otide translations and from a eukaryotic and not a prokaryotic species. 3) The algorithm options used with BLAST were not exactly the same. A) Moreno-Hagelsieb and Latimer used the blastpgp algorithm from the NCBI [35] BLAST, which has the Smith-Waterman -s T option available. B) In this work blastall using blastx (carp vs. human) and tblastn (human vs. carp) were used. The -s T option is only avail- able for tblastn and not blastx with NCBI blastall. Note: FTihgisufriegu2re summarises the number of successful RBHs found using different BLAST options This figure summarises the number of successful RBHs found using different BLAST options. It can be seen that soft filtering (-F "m S") makes a significant difference to the number of successful RBHs attained. The Smith-Waterman algo- rithm, on the other hand, made little difference to the number of successful RBHs. The results of each filtering option were normalised to the default options of BLAST (-F T -s F). Page 4 of 17 (page number not for citation purposes)