Comparison of percent identity, alignment length and mismatches given by SMAT80 and BLOSUM90 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 BLOSUM90 matrix. The best non-self hits common to both matrices were filtered out from these BLAST results. The percent identity, alignment length and number of mismatches were divided in two categories- better or poor using SMAT80 compared to BLOSUM90 and the numbers of proteins for these categories were calculated. We see here a more number of proteins belonging to better category in each case.