Additional file 3.

Supplementary Figure 1: Comparison of E-values & bit scores given by SMAT80 and BLOSUM62 matrices BLAST searches were performed against non-redundant (nr) database for nine Apicomplexan species (the labels on X-axis: Pberghei for Plasmodium berghei, Pchabaudi for Plasmodium chabaudi, Pknowlesi for Plasmodium knowlesi, Pvivax for Plasmodium vivax, Pyoelii for Plasmodium yoelii yoelii, Tgondii for Toxoplasma gondii, Cparvum for Cryptosporidium parvum, Ncaninum for Neospora caninum and Tparva for Theileria parva) using SMAT80 and BLOSUM62 matrix. The best non-self hits common to both matrices from these BLAST results were divided in eight categories shown in the legend at topleft position of figure. The percentage for each category was calculated and it was observed that most of the apicomplexan proteins fall in first two categories that means most of apicomplexan proteins give better or similar E-values and better bit scores with SMAT80 compared to BLOSUM62 matrix.

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Ali et al. BMC Genomics 2011 12(Suppl 3):S6   doi:10.1186/1471-2164-12-S3-S6