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This article is part of the supplement: Tenth International Conference on Bioinformatics. First ISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011): Computational Biology

Open Access Proceedings

ApicoAlign: an alignment and sequence search tool for apicomplexan proteins

Jamshaid Ali, Umadevi Paila and Akash Ranjan*

Author Affiliations

Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, A Sun Centre of Excellence in Medical Bioinformatics, Hyderabad 500001, India

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BMC Genomics 2011, 12(Suppl 3):S6  doi:10.1186/1471-2164-12-S3-S6

Published: 30 November 2011

Additional files

Additional file 1:

Supplementary Table S1: Similarities in amino acid composition for different apicomplexan species T-test P-values (two-tailed ) for the amino acid frequency of all 20 amino acids across proteins of P. falciparum vs. Mycobacterium tuberculosis (control) and other Apicomplexans orthologs.

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Additional file 2:

Supplementary Table S2: Performance of SMAT80 over BLOSUM90 for different apicomplexan species against non-redundant database The E-values and bits scores of non-self best hits commmon to SMAT80 and BLOSUM90 were compared for P. berghei (sheet1), P. chabaudi (sheet2), P. knowlesi (sheet3), P. vivax (sheet4), P. yoelii yoelii (sheet5), Toxoplasma gondii (sheet6), Cryptosporidium parvum (sheet7), Neospora caninum (sheet8) and Theileria parva (sheet9).

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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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Additional file 4:

Supplementary Figure 2 Comparison of percent identity, alignment length and mismatches 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 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 BLOSUM62 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.

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Additional file 5:

Supplementary Figure 3: Comparison of SMAT with BLOSUM series in terms of Best Bidirectional Hits (BBH) The Best Bidirectional Hits (BBHs) were extracted from BLAST results of nine apicomplexan species studied here against Arabidopsis thaliana using BLOSUM62, BLOSUM90, SMAT50, SMAT60, SMAT70, SMAT80 and SMAT90 matrices. The colour of the bar corresponds to the matrix in the legend at topleft position of figure using which BBHs were calculated.

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Additional file 6:

Supplementary Figure 4: Number of Best Bidirectional Hits (BBHs) uniquely obtained by SMAT but not by BLOSUM90 The numbers of Best Bidirectional Hits (BBHs) of nine apicomplexan species were calculated against Arabidopsis thaliana which are detected by using SMAT50 but not by BLOSUM90 and vice-versa. Similarly BBHs uniquely detected by SMAT60, SMAT70, SMAT80 and SMAT90 matrices but not by BLSOUM90 and vice-versa were calculated. In P. vivax, T. gondii, C. parvum, N. caninum and T. parva BLOSUM90 gives slightly higher number of unique BBHs compared to SMAT50 but for rest other cases SMAT matrices generally pick higher number of unique BBHs.

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Additional file 7:

Supplementary Figure 5: Best Bidirectional Hits (BBH) for proteins of different plasmodia using SMAT80 and BLOSUM matrices The Best Bidirectional Hits (BBHs) were extracted from BLAST results of six Plasmodium species: Plasmodium berghei (Pb), Plasmodium chabaudi (Pc), Plasmodium falciparum (Pf), Plasmodium knowlesi (Pk), Plasmodium vivax (Pv) and Plasmodium yoelii yoelii (Py) using SMAT80, BLOSUM90 and BLOSUM62 matrices. The labels on x-axis are two letter abbreviation of organism followed by name of the matrix used like Pb_SMAT80 means number of BBHs for Plasmodium berghei using SMAT80 matrix. The colour of the bar corresponds to the organism in the legend at top right position of figure against which BBHs were calculated.

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Additional file 8:

Supplementary Figure 6: Best Bidirectional Hits (BBH) for apicomplexan proteins other than plasmodia using SMAT80 and BLOSUM matrices The Best Bidirectional Hits (BBHs) were extracted from BLAST results of four apicomplexan species: Toxoplasma gondii (Tg), Cryptosporidium parvum (Cp), Neospora caninum (Nc) and Theileria parva (Tp) using SMAT80, BLOSUM90 and BLOSUM62 matrices. The labels on x-axis are two letter abbreviation of organism followed by name of the matrix used like Tg_SMAT80 means number of BBHs for Toxoplasma gondii using SMAT80 matrix. The colour of the bar corresponds to the organism in the legend at top right position of figure against which BBHs were calculated.

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Additional file 9:

Supplementary Figure 7: Alignment extension of experimentally characterized P. falciparum GST with PfFSmat60 matrix The sequences compared here are the experimentally characterized Glutathione S-transferase (GST) of P. falciparum, PF14_0187 and yeast Gtt2p (Glutathione S-transferase capable of homodimerization, gi:6322968). (a) The alignment with BLOSUM50 was only 22 amino acids (59 to 79 for query and 72 to 93 for subject). (b) A significantly improved alignment of 233 (1 to 209 for query and 15 to 232 for subject) amino acids is achieved using PfFSmat60 matrix. The fasta program (FASTA package, version 3) was used for alignment.

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Additional file 10:

Supplementary Figure 8: Alignment extension of experimentally characterized P. falciparum kinase with PfFSmat60 matrix The sequences compared are the experimentally characterized P. falciparum protein kinase (PF11_0220) and PIK-related protein kinase and rapamycin target of Saccharomyces cerevisiae (gi: 6322526). While BLOSUM50 gave an alignment score of 23.4 bits at an E-value 0.31 with an overlap of only 71 amino acid residues (637-707:2090-2157), PfFSmat60 gave an alignment score of 4872.5 bits at an E-value 0.0 and the overlap was 1990 amino acid residues (1-1675:375-2307). The fasta program (FASTA package, version 3) was used for alignment.

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Additional file 11:

Supplementary Table S5: Pairwise alignments of Cyptosporidium parvum ACBP1 (cgd1_1140) against Arabidopsis thaliana ACBP1 (gi:15238757) The pairwise alignment was performed between two experimentally characterized proteins Cyptosporidium parvum ACBP1 (cgd1_1140) and Arabidopsis thaliana ACBP1 (gi:15238757) using water program (EMBOSS package) and FASTA program.

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Additional file 12:

Supplementary Figure 9: Alignment extension of probable P. chabaudi bi-functional enzyme of the shikimate pathway The sequences compared here are the P. chabaudi hypothetical protein, PCHAS_041350 and yeast multifunctional protein, Aro1p (gi:6320332). (a) The alignment with BLOSUM50 showing the aligned motif regions for only EPSP synthase I motif (gray shading). (b) The alignment extended by PfFSmat60 for both the EPSP synthase I and shikimate kinase motifs represented as (i) and (ii) respectively. The fasta program (FASTA package, version 3) was used for alignment.

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Additional file 13:

Supplementary Figure 10: Alignment extension of probable P. knowlesi bi-functional enzyme of the shikimate pathway The sequences compared here are the P. knowlesi hypothetical protein, PKH_041350 and yeast multifunctional protein, Aro1p (gi:6320332). (a) The alignment with BLOSUM50 showing the aligned motif regions for only EPSP synthase I motif (gray shading). (b) The alignment extended by PfFSmat60 for both the EPSP synthase I and shikimate kinase motifs represented as (i) and (ii) respectively. The fasta program (FASTA package, version 3) was used for alignment.

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Additional file 14:

Supplementary Figure 11: Alignment extension of probable P. vivax bi-functional enzyme of the shikimate pathway The sequences compared here are the P. vivax hypothetical protein, PVX_003750 and yeast multifunctional protein, Aro1p (gi:6320332). (a) The alignment with BLOSUM50 showing the aligned motif regions for only EPSP synthase I motif (gray shading). (b) The alignment extended by PfFSmat60 for both the EPSP synthase I and shikimate kinase motifs represented as (i) and (ii) respectively. The fasta program (FASTA package, version 3) was used for alignment.

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Additional file 15:

Supplementary Figure 12: Alignment extension of probable P. yoelii bi-functional enzyme of the shikimate pathway The sequences compared here are the P. yoelii hypothetical protein, PY00069 and yeast multifunctional protein, Aro1p (gi:6320332). (a) The alignment with BLOSUM50 showing the aligned motif regions for only EPSP synthase I motif (gray shading). (b) The alignment extended by PfFSmat60 for both the EPSP synthase I and shikimate kinase motifs represented as (i) and (ii) respectively. The fasta program (FASTA package, version 3) was used for alignment.

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Additional file 16:

Supplementary Table S4: Pairwise alignments of probable plasmodia bifunctional proteins of shikimate pathway with yeast AROM complex The pairwise alignments of probable plasmodia bifunctional proteins of shikimate pathway with yeast AROM complex using water program (EMBOSS package) and FASTA program.

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Additional file 17:

Supplementary Table S3: Pairwise alignments of MAL7P1.156 against four known yeast triglyceride lipases The table shows the E-values, bits scores and alignment length of pairwise alignments between probable P. falciparum acyl glycerol lipase (MAL7P1.156) and four known yeast triglyceride lipases (tgl2p, tgl3p, tgl4p and tgl5p).

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Additional file 18:

Supplementary Figure 13: Alignment of probable missing enzyme of P. falciparum glycerol biosynthesis pathway The sequences compared are conserved protein in Plasmodium sps. with unknown function, MAL7P1.156 and yeast triacylglycerol lipase tgl5p which has patatin domain for lipase activity spanning 183 to 388 residues. (a) The alignment with BLOSUM50 covered only few residues of patatin domain (grey shaded). (b) The alignment generated with PfFSmat60 covered whole patatin domain of subject sequence. The fasta program (FASTA package, version 3) was used for alignment.

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