ApicoAlign: an alignment and sequence search tool for apicomplexan proteins

Ali, Jamshaid; Paila, Umadevi; Ranjan, Akash

doi:10.1186/1471-2164-12-s3-s6

Cited by 7 publications

(17 citation statements)

References 18 publications

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“…In our earlier studies [9,10] and this study, we have demonstrated that SMAT80 gave better E-values and better bit scores for most of the apicomplexan proteins. Next, we were interested to know whether parasite specific matrices would give poor E-values and/or bit scores for the proteins for which orthologs must not exist (in biological context) in a particular family/class of Apicomplexa.…”

Section: Resultssupporting

confidence: 59%

“…However we have shown that the choice of matrices can also significantly improve the ortholog detection in our previous [9,10] and the present studies. SMAT80 uniquely detected orthologs for 16, 166, 11, 21, 32, 72, 31, 185, 717, 7, 3, 5, 291, 20 and 191 proteins of Babesia bovis, Theileria annulata, Theileria parva, P. berghei, P. chabaudi, P. falciparum, P. knowlesi, P. vivax, P. yoelii yoelii, Cryptosporidium hominis, Cryptosporidium muris, Cryptosporidium parvum, Eimeria tenella, Neospora caninum and Toxoplasma gondii respectively (Figure 4).…”

Section: Resultssupporting

confidence: 58%

“…a novel series of substitution matrices (SMAT and PfFSmat60) and demonstrated their superior performance over the standard matrices (BLOSUM and PAM) for P. falciparum proteins in particular [9] and for apicomplexan proteins in general [10]. We further demonstrated that the amino acid compositions of proteins of nine apicomplexan parasites ( Toxoplasma gondii, Neospora caninum, Theileria parva, Cryptosporidium parvum, P. berghei, P. chabaudi, P. knowlesi, P. vivax and P. yoelii yoelii ) were similar to that of P. falciparum and because of this unusual amino acid composition of apicomplexan proteins these matrices (originally developed for P. falciparum ) performed better even for other apicomplexan proteins (when compared to standard matrices BLOSUM & PAM) [10]. Moreover to provide access to this novel series of matrices to researchers working on apicomplexan parasites, a web server ApicoAlign (http://www.cdfd.org.in/apicoalign/) was developed to detect orthologs and align apicomplexan proteins [10].…”

Section: Introductionmentioning

confidence: 99%

“…We further demonstrated that the amino acid compositions of proteins of nine apicomplexan parasites ( Toxoplasma gondii, Neospora caninum, Theileria parva, Cryptosporidium parvum, P. berghei, P. chabaudi, P. knowlesi, P. vivax and P. yoelii yoelii ) were similar to that of P. falciparum and because of this unusual amino acid composition of apicomplexan proteins these matrices (originally developed for P. falciparum ) performed better even for other apicomplexan proteins (when compared to standard matrices BLOSUM & PAM) [10]. Moreover to provide access to this novel series of matrices to researchers working on apicomplexan parasites, a web server ApicoAlign (http://www.cdfd.org.in/apicoalign/) was developed to detect orthologs and align apicomplexan proteins [10]. In the present study, we assess the performance of these matrices with that of compositionally adjusted matrices (sensitive PSI-BLAST searches) in terms of detection of the true and false positives, an important aspect missing in our earlier studies [9,10].…”

Section: Introductionmentioning

confidence: 99%

“…Moreover to provide access to this novel series of matrices to researchers working on apicomplexan parasites, a web server ApicoAlign (http://www.cdfd.org.in/apicoalign/) was developed to detect orthologs and align apicomplexan proteins [10]. In the present study, we assess the performance of these matrices with that of compositionally adjusted matrices (sensitive PSI-BLAST searches) in terms of detection of the true and false positives, an important aspect missing in our earlier studies [9,10]. Many protein families like kinases are under-represented in apicomplexan parasites probably because standard matrices (BLOSUM & PAM) could not detect them during genome annotation.…”

Section: Introductionmentioning

confidence: 99%

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The parasite specific substitution matrices improve the annotation of apicomplexan proteins

2012

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Background A number of apicomplexan genomes have been sequenced successfully in recent years and this would help in understanding the biology of apicomplexan parasites. The members of the phylum Apicomplexa are important protozoan parasites (Plasmodium, Toxoplasma and Cryptosporidium etc) that cause some of the deadly diseases in humans and animals. In our earlier studies, we have shown that the standard BLOSUM matrices are not suitable for compositionally biased apicomplexan proteins. So we developed a novel series (SMAT and PfFSmat60) of substitution matrices which performed better in comparison to standard BLOSUM matrices and developed ApicoAlign, a sequence search and alignment tool for apicomplexan proteins. In this study, we demonstrate the higher specificity of these matrices and make an attempt to improve the annotation of apicomplexan kinases and proteases. Results The ROC curves proved that SMAT80 performs best for apicomplexan proteins followed by compositionally adjusted BLOSUM62 (PSI-BLAST searches), BLOSUM90 and BLOSUM62 matrices in terms of detecting true positives. The poor E-values and/or bit scores given by SMAT80 matrix for the experimentally identified coccidia-specific oocyst wall proteins against hematozoan (non-coccidian) parasites further supported the higher specificity of the same. SMAT80 uniquely detected (missed by BLOSUM) orthologs for 1374 apicomplexan hypothetical proteins against SwissProt database and predicted 70 kinases and 17 proteases. Further analysis confirmed the conservation of functional residues of kinase domain in one of the SMAT80 detected kinases. Similarly, one of the SMAT80 detected proteases was predicted to be a rhomboid protease. Conclusions The parasite specific substitution matrices have higher specificity for apicomplexan proteins and are helpful in detecting the orthologs missed by BLOSUM matrices and thereby improve the annotation of apicomplexan proteins which are hypothetical or with unknown function.

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Section: Resultssupporting

confidence: 59%

Section: Resultssupporting

confidence: 58%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The parasite specific substitution matrices improve the annotation of apicomplexan proteins

2012

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Substitution Matrices

Altschul

2013

Encyclopedia of Life Sciences

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A substitution matrix is a collection of scores for aligning nucleotides or amino acids with one another. These scores generally represent the relative ease with which one nucleotide or amino acid may mutate into or substitute for another, and they are used to measure similarity in sequence alignments. Substitution matrices are used in conjunction with gap costs to construct local or global alignments. A local alignment substitution matrix implicitly corresponds to a set of target frequencies for aligned letters, which characterise the alignments the matrix may most easily distinguish from chance. Thus different substitution matrices are optimal for comparing related sequences that have diverged to differing degrees. The point accepted mutation and blocks substitution matrix (BLOSUM) series of matrices for protein sequence comparison have been derived from collections of related sequences. Special‐purpose matrices may be appropriate for comparing sequences with biased nucleotide or amino acid composition. Key Concepts: Match/mismatch scores generally are suboptimal for comparing protein sequences. A log‐odds substitution matrix is characterised by its target frequencies and scale. All local‐alignment substitution matrices are implicitly log‐odds matrices. Different substitution matrices are tailored to different degrees of evolutionary divergence. Amino acid substitution matrices are constructed from curated sets of alignments. The sequence divergence for which a substitution matrix is tailored may be measured by relative entropy. Special matrices may be preferred for comparing sequences with nonstandard nucleotide or amino acid composition. For gapped local alignments, statistical parameters must be estimated by random simulation. For protein‐coding DNA, distant relationships are more easily detected at the protein than at the DNA level. For global alignments, an equivalent scoring system results from adding 2 x to all substitution scores, and x to the score for each letter aligned with a null.

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India’s Computational Biology Growth and Challenges

Chakraborty

Bandyopadhyay

Agoramoorthy

2016

Interdiscip Sci Comput Life Sci

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India's computational science is growing swiftly due to the outburst of internet and information technology services. The bioinformatics sector of India has been transforming rapidly by creating a competitive position in global bioinformatics market. Bioinformatics is widely used across India to address a wide range of biological issues. Recently, computational researchers and biologists are collaborating in projects such as database development, sequence analysis, genomic prospects and algorithm generations. In this paper, we have presented the Indian computational biology scenario highlighting bioinformatics-related educational activities, manpower development, internet boom, service industry, research activities, conferences and trainings undertaken by the corporate and government sectors. Nonetheless, this new field of science faces lots of challenges.

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ApicoAlign: an alignment and sequence search tool for apicomplexan proteins

Cited by 7 publications

References 18 publications

The parasite specific substitution matrices improve the annotation of apicomplexan proteins

The parasite specific substitution matrices improve the annotation of apicomplexan proteins

Substitution Matrices

India’s Computational Biology Growth and Challenges

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