Sequence alignment is one of the basic problems in computational biology that has helped researchers analyze biological sequences. The analysis has helped biologists to detect pathogens ;to develop drugs, and to predict the secondary and tertiary structure of a protein and identity common genes. The objective of the Phylogenetic tree is to determine the branch length and to figure out how the evolutionary tree has been generated . One way to tackle MSA is to use Hidden Markov Models (HMMs), which are known to be very powerful in the related problem domain of speech recognition. The fully trained model is applied to draw a valid conclusion about the evaluation of malarial parasites

Bandyopadhyay, Raktima

Mujaffor, Sk.

Swarnkar, Tripti

English

Interscience Research Network

International Journal of Computer and Communication Technology Volume 1 Issue 3 Article 6 July 2010 Sequence Alignment and Phylogenetic Tree Construction of Malarial Parasites Sk. Mujaffor M.Tech (2nd Yr.), ITER, S´O´A University, mujaffor09@yahoo.in Tripti Swarnkar Deptt. Of CA, SOA University Bhubaneswar, tripti_sarap@yahoo.com Raktima Bandyopadhyay Dept. of Bioinformatics, Vidyasagar University, raktima.bioinformatics@gmail.com Follow this and additional works at: https://www.interscience.in/ijcct Recommended Citation Mujaffor, Sk.; Swarnkar, Tripti; and Bandyopadhyay, Raktima (2010) "Sequence Alignment and Phylogenetic Tree Construction of Malarial Parasites," International Journal of Computer and Communication Technology: Vol. 1 : Iss. 3 , Article 6. DOI: 10.47893/IJCCT.2010.1042 Available at: https://www.interscience.in/ijcct/vol1/iss3/6 This Article is brought to you for free and open access by the Interscience Journals at Interscience Research Network. It has been accepted for inclusion in International Journal of Computer and Communication Technology by an authorized editor of Interscience Research Network. For more information, please contact sritampatnaik@gmail.com. Sequence Alignment and Phylogenetic Tree Construction of Malarial Parasites  Sequence Alignment and Phylogenetic Tree Construction of Malarial ParasitesSk. Mujaffor1 , Tripti Swarnkar2 , Raktima Bandyopadhyay3M.Tech (2nd Yr.), ITER, S´O´A University  mujaffor09 @ yahoo.in Department of Computer Applications Institute of Technical Education & Research, S´O´A University, Bhubaneswar tripti_sarap@yahoo.comDept. of Bioinformatics, Vidyasagar University raktima.bioinformatics@gmail.comAbstract-Sequence alignment is one of the basic problems in computational biology that has helped researchers analyze biological sequences. The analysis has helped biologists to  detect pathogens ;to  develop drugs, and to predict the secondary and tertiary structure of a protein and identity common genes.  The objective of the Phylogenetic tree is to determine the branch length and to figure out how the evolutionary  tree has been generated . One way to tackle MSA is to use Hidden Markov Models (HMMs), which are known to be very powerful in the related problem domain of speech recognition. The fully trained model is applied to draw a valid conclusion about the evaluation of malarial parasites.Keywords- Sequence alignment; Phylogenetic tree; HMM; MSA;  ClustalW; Merozoite surface protein; BioEdit I. INTRODUCTION Multiple sequence alignment (MSA) [5] of nucleotides (or amino acids) is one of the basic problems in computational biology. Good alignments allow sequence comparison, which can be used for a variety of purposes, such as to determine the phylogenetic relatedness of organisms, to identify conserved motifs and to assist secondary and tertiary structure prediction. Through the sequence alignment it can be resolved about the transmission of disease by parasites. Zoonosis is a term that means transmission of a disease from subhuman vertebrate to human body. For the evolution of parasite and the evolution of parasitic disease, the study of Zoonosis is very important in respect to the epidemiology of the disease. India is endemic for malaria and it’s a global problem also. Human malaria is basically caused by four  parasites – Plasmodium vivax, Plasmodium falciparum, Plasmodium ovale and Plasmodium  malariae. Plasmodium cynomolgi is a malerial parasite of monkey and Plasmodium berghei is the rodent parasite. Our objective is to find out the Zoonosis of malerial parasites. A.. Sequences in the realm of a biologist A sequence for a biologist is either a RNA, DNA or protein string made of their respective alphabet set shown below : DNA = { A, C, G, T } RNA = { A, C, G, U } Protein = { A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V } B. Sequence Alignment A Sequence alignment [1] means lining up the characters of strings, allowing mismatches as well as matches and allowing characters of one string to be placed opposite spaces made in opposing strings. Our objective is to find the regions of similarity which may provide additional information on the functional, structural, evolutionary and other interests between the sequences. C. Phylogenetic Tree The similarity of molecular mechanisms of the organisms that have been studied  strongly suggests that all organisms on Earth had a common ancestor. Thus any set of species is related, and this relationship is called a phylogeny. Usually the relationship can be represented by a phylogenetic tree [4] . The task 180International Journal of Computer and Communication Technology (IJCCT), ISSN: 2231-0371, Vol-1, Iss-3Sequence Alignment and Phylogenetic Tree Construction of Malarial Parasites  of phylogenetics is to infer this tree from observations upon the existing organisms. D.   Hidden Markov Model A hidden Markov model (HMM) [5 ] is a statistical model in which the system being modeled is assumed to be a Markov process with unobserved state. In a regular Markov model, the state is directly visible to the observer, and therefore the state transition probabilities are the only parameters. In a hidden Markov model, the state is not directly visible, but output dependent on the state is visible. Each state has a probability distribution over the possible output tokens. Therefore the sequence of tokens generated by an HMM gives some information about the sequence of states. Note that the adjective 'hidden' refers to the state sequence through which the model passes, not to the parameters of the model; Even if the model parameters are known exactly, the model is still 'hidden'. There are three canonical problems associated with HMM: Given the parameters of the model, compute the probability of a particular output sequence. This requires summation over all possible state sequences, but can be done efficiently using the forward algorithm, which is a form of dynamic programming.Given the parameters of the model and a particular output sequence, find the state sequence that is most likely to have generated that output sequence. This requires finding a maximum over all possible state sequences, but can similarly be solved efficiently by the Viterbi algorithm.Given an output sequence or a set of such sequences, find the most likely set of state transition and output probabilities. In other words, derive the maximum likelihood estimate of the parameters of the HMM given a dataset of output sequences. No tractable algorithm is known for solving this problem exactly, but a local maximum likelihood can be derived efficiently using the Baum-Welch algorithmor the Baldi-Chauvin algorithm.The Baum-Welch algorithm is also known as the forward-backward algorithm, and is a special case of the Expectation-maximization algorithm.E.  Multiple Sequence Alignment Multiple Sequence Alignment (MSA), is an extension of two-sequence/pairwise sequence alignment . Nowadays, multiple sequence alignment is an important tool in molecular biology and it provides key information for sequence analysis. There are several uses of MSA; finding sequence to determine patterns that characterize protein/gene families; detecting homology between new sequences and known protein/gene family sequences; predicting secondary and tertiary structures of new protein sequences; predicting function of new sequences and molecular evolutionary analysis . F. ClustalW ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. It is also based on HMM.  It produces biologically meaningful multiple sequence alignment of divergent sequences[3]. It calculates the best match for the selected sequences and lining them up so that the identities, similarities and differences can be seen. Evolutionary relationship can be seen via viewing cladograms or phylograms. G. Merozoite surface protein A merozoite surface protein is a protein molecule taken from the surface of a merozoite. Merozoite surface proteins are used in researching malaria, caused by protozoans.  H. BioEdit BioEdit is a biological sequence editor that runs in Windows 95/ 98/ 2000 and is intended to provide basic functions for protein and nucleic sequence editing, alignment, manipulation and analysis. It offers a graphical interface for users to run external analysis programs  II. MATERIALS OF METHOD 181International Journal of Computer and Communication Technology (IJCCT), ISSN: 2231-0371, Vol-1, Iss-3Sequence Alignment and Phylogenetic Tree Construction of Malarial Parasites  The sequences of merozoite surface protein of the malarial parasites i.e.  Plasmodium vivax, Plasmodium falciparum, Plasmodium berghei, Plasmodium cynomolgi were downloaded from National Center for Biotechnology Information ( NCBI).The sequences were FASTA [2] formatted and multiple sequence alignment was done by using ClustalW . It was also determined about the amino acid composition of the merozoite surface protein of all the parasites by BioEdit. Phylogenetic tree was constructed. The sequences of malaria parasites are A. Plasmodium berghei MKVIGLLFSFVFFAIKCKSETIEVYNDIIQKLEKLESLSVEGLELFQKSQVIINASPPSETINPFSDNTFAPKLQGFITP……………………….. …………………………………………………. B. Plasmodium cynomolgi MKALLFLFSFIFFVTKCQCETEDYKQLLVKLDKLEALVVDGYELFQKKKLEVKDIPVDNNANENNVNSLAYKIR……………………….…………………………………………………. C. Plasmodium falciparum FINNAYNMSIRRSMAESKTPTGAGGSGSAGGSGSAGGSGSAGGSGSAGSTTTTNDAEASTSTSSENPNHNNAET…………………………………………….…………………………………………D Plasmodium vivax EIYDLAQEIRKNENKLIVENKFDFSGVVELQVQKVLIIKKIEALKNVQNLLKNAKVKDDLYVPKVYKTGEKPEPYYLMVLKREIDKLKD………………………………………………… ………………………………………………… III. RESULT DISCUSSION From the sequence alignment and phylogenetic tree construction it has been observed that there is a very close relationship between Plasmodium cynomolgi and Plasmodium vivax ( Max score, Total score, Query coverage and E-value). It has shown below : Accession Description MaxscoreTotalscoreQuerycoverageEvalueBAF74064.1merozoite surface protein-1 [Plasmodium cynomolgi] 36453645 100% 0.0 BAF74054.1merozoite surface protein-1 [Plasmodium cynomolgi] 28872887 100% 0.0 BAF74055.1merozoite surface protein-1 [Plasmodium cynomolgi] 28662866 100% 0.0 BAF74060.1merozoite surface protein-1 [Plasmodium cynomolgi] 28622862 100% 0.0 BAI82251.1merozoite surface protein 1 [Plasmodium cynomolgi] 28562856 98% 0.0 AAN86210.1merozoite surface protein 1 [Plasmodium vivax] >gb|AAN86225.1|AF435612_1 merozoite surface protein 1 [Plasmodium vivax] 22872287 98% 0.0 AAN86235.1merozoite surface protein 1 [Plasmodium vivax] >gb|AAN86239.1|AF435629_1 merozoite surface protein 1 [Plasmodium vivax] 22742274 98% 0.0 AAN86238.1merozoite surface protein 1 [Plasmodium vivax] >gb|AAN86241.1|AF435631_1 merozoite surface protein 1 [Plasmodium vivax] 22692269 98% 0.0 AAN86215.1merozoite surface protein 1 [Plasmodium vivax] >gb|AAN86216.1|AF435603_1 merozoite surface 22662266 98% 0.0 182International Journal of Computer and Communication Technology (IJCCT), ISSN: 2231-0371, Vol-1, Iss-3Sequence Alignment and Phylogenetic Tree Construction of Malarial Parasites  Accession Description MaxscoreTotalscoreQuerycoverageEvalueprotein 1 [Plasmodium vivax] A. Alignments dbj|BAF74064.1|  merozoite surface protein-1 [Plasmodium cynomolgi] Length=1786,   Score = 3645 bits (9453),  Expect = 0.0, Method: Compositional matrix adjust.  Identities = 1786/1786 (100%), Positives = 1786/1786 (100%), Gaps = 0/1786 (0%) Query  1      MKALLFLFSFIFFVTKCQCETEDYKQLLVKLDKLEALVVDGYELFQKKKLEVKDIPVDNN  60 MKALLFLFSFIFFVTKCQCETEDYKQLLVKLDKLEALVVDGYELFQKKKLEVKDIPVDNNSbjct  1      MKALLFLFSFIFFVTKCQCETEDYKQLLVKLDKLEALVVDGYELFQKKKLEVKDIPVDNN  60 ………………………………………….…………………………………………dbj|BAD08401.1|  merozoite surface protein 1 [Plasmodium falciparum] Length=1688  Score = 1084 bits (2804),  Expect = 0.0, Method: Compositional matrix adjust.  Identities = 707/1888 (37%), Positives = 1037/1888 (54%), Gaps = 311/1888 (16%) Query  1      MKALLFLFSFIFFVTKCQCET-EDYKQLLVKLDKLEALVVDGYELFQKKKLEVKD-----  54 MK + FL SF+FF+   QC T E Y++L+ KL+ LE  V+ GY LFQK+K+ +KD      Sbjct  1      MKIIFFLCSFLFFIINTQCVTHESYQELVKKLEALEDAVLTGYSLFQKEKMVLKDGANTQ  60 …………………………………………………………………………………..gb|AAN86210.1|AF435596_1  merozoite surface protein 1 [Plasmodium vivax] gb|AAN86225.1|AF435612_1  merozoite surface protein 1 [Plasmodium vivax] Length=1728,  Score = 2287 bits (5927),  Expect = 0.0, Method: Compositional matrix adjust.  Identities = 1241/1773 (69%), Positives = 1391/1773 (78%), Gaps = 82/1773 (4%) Query  1      MKALLFLFSFIFFVTKCQCETEDYKQLLVKLDKLEALVVDGYELFQKKKLEVKDIPVDNN  60 MKALLFLFSFIFFVTKCQCETE YKQL+ KLDKLEALVVDGYELF KKKL   DI V+ N Sbjct  1      MKALLFLFSFIFFVTKCQCETESYKQLVAKLDKLEALVVDGYELFHKKKLGENDIKVEAN  60 ………………………………………………….. …………………………………………………. B. Phylogenetic Tree The phylogenetic trees made by Neighbour Joining method, Maximum parsimony method, Unweighted pair group method with arithmetic mean ( UPGMA method ), Minimum Evolutionary distance method ( ME method)are shown by figure no. 2, 3, 4 and 5 respectively. 183International Journal of Computer and Communication Technology (IJCCT), ISSN: 2231-0371, Vol-1, Iss-3Sequence Alignment and Phylogenetic Tree Construction of Malarial Parasites      Fig.2     Fig.3          Fig.4     Fig.5 C. Amino acid composition - BioEdit The amino acid composition of four malarial parasites are Plasmodium berghei, Plasmodium cynomolgi, Plasmodium falciparum and Plasmodium vivax shown by figure no. 6,7,8 and 9 respectively.   Fig.6  Fig.7     Fig.8     Fig.9 Protein: Plasmodium berghei Length = 1787 amino acids Molecular Weight = 198146.17 Daltons Amino Acid Number          Mol% Ala  A 139 7.78 Cys  C 19 1.06 Asp  D 74 4.14 Glu  E 160 8.95 Phe  F 52 2.91 Gly  G 80 4.48 His  H 12 0.67 Ile  I 118 6.60 Lys  K 176 9.85 Leu  L 152 8.51 Met  M 21 1.18 Asn  N 128 7.16 184International Journal of Computer and Communication Technology (IJCCT), ISSN: 2231-0371, Vol-1, Iss-3Sequence Alignment and Phylogenetic Tree Construction of Malarial Parasites  Pro  P 90 5.04 Gln  Q 66 3.69 Arg  R 39 2.18 Ser  S 134 7.50 Thr  T 169 9.46 Val  V 79 4.42 Trp  W 1 0.06 Tyr  Y 78 4.36 Protein: Plasmodium cynomolgi Length = 1786 amino acids Molecular Weight = 198841.67 Daltons Amino Acid Number Mol%   Ala  A  153 8.57   Cys  C  19 1.06   Asp  D  94 5.26   Glu  E  170 9.52   Phe  F  46 2.58   Gly  G  90 5.04   His  H  24 1.34   Ile  I  97 5.43   Lys  K  206 11.53   Leu  L  171 9.57   Met  M  34 1.90   Asn  N  112 6.27   Pro  P  89 4.98   Gln  Q  71 3.98   Arg  R  28 1.57   Ser  S 96 5.38   Thr  T   121 6.77   Val  V   88 4.93   Trp  W   3 0.17   Tyr  Y   74 4.14 Protein: Plasmodium falciparum Length = 196 amino acids Molecular Weight = 19665.25 Daltons Amino AcidNumber Mol%   Ala  A      22 11.22   Cys  C      0 0.00   Asp  D      6 3.06   Glu  E      13 6.63   Phe  F      1 0.51   Gly  G      24 12.24   His  H      5 2.55   Ile  I      2 1.02   Lys  K      8 4.08   Leu  L      1 0.51   Met  M      3 1.53   Asn  N      23 11.73   Pro  P      14 7.14   Gln  Q      15 7.65   Arg  R      4 2.04   Ser  S      28 14.29   Thr  T      23 11.73   Val  V      3 1.53   Trp  W      0 0.00 Protein: Plasmodium vivax Length = 338 amino acids Molecular Weight = 37344.74 Daltons Amino Acid Number Mol%   Ala  A     35 10.36   Cys  C     2 0.59   Asp  D     15 4.44   Glu  E     25 7.40   Phe  F     7 2.07   Gly  G     13 3.85   His  H     4 1.18   Ile  I     18 5.33   Lys  K     36 10.65   Leu  L     28 8.28   Met  M     7 2.07   Asn  N     21 6.21   Pro  P     19 5.62   Gln  Q     26 7.69   Arg  R     3 0.89   Ser  S     16 4.73 7.69     23 6.80 0.00     26    Trp  W     0    Tyr  Y     14 4.14 D. The Pairwise evolutionary distance are shown below:Title: para Description   No. of Taxa : 4   Data File : para   Data Title : para   Data Type : Amino acid   Analysis : Disparity Index Analysis   Calculate : Conduct ID-Test (1000 reps; seed=86348)   Include Sites    ->Gaps/Missing Data : Complete Deletion No. of Sites : 193   Prob (black) : Probability computed (must be <0.05 for hypothesis rejection at 5% level [yellow background])   Stat (blue) : Disparity Index. [1] #Plasmodium_berghei [2] #Plasmodium_cynomolgi [3] #Plasmodium_falciparum [4] #Plasmodium_vivax [          1        2        3        4 ] [1]           [ 1.119 ][ 3.150 ][ 1.415 ] [2]    0.001           [ 2.539 ][ 0.337 ] [3]    0.000    0.000           [ 2.430 ] [4]    0.000    0.018    0.000 185International Journal of Computer and Communication Technology (IJCCT), ISSN: 2231-0371, Vol-1, Iss-3Sequence Alignment and Phylogenetic Tree Construction of Malarial Parasites  .IV. CONCLUSION Among the four human malarial parasites only Plasmodium vivax was found to be very close to monkey parasite i.e, Plasmodium cynomolgi. So it may be predicted that malaria was transmitted from monkey to man. As a case of Zoonosis, the Plasmodium cynomolgi might be mutated and modified in such a way so that it could adapt to the human body and ultimately established a human parasite. V. REFERENCES [1]   A. L. Delcher, et al., "Alignment of whole genomes,"               Nucl. Acids Research, vol. 27, pp. 2369-2376, 1999.      [2]   D. Gusfield, Algorithms on Strings, Trees and          Sequences:Computer cience and Computational         Biology .Cambridge University Press, 1997. [3]   M. Tompa, "Lecture notes on Biological Sequence          Analysis," University of Washington, Seattle, Technical          report, 2000. [4]   Neil C. Jones and Pavel A. Pevzner, 2004 –“An        Introduction toBioinformatics Algorithms”.[5]   Richard Durbin,Eddy, Mitchison, 1998-“Biological         Sequence Analysis”. 186International Journal of Computer and Communication Technology (IJCCT), ISSN: 2231-0371, Vol-1, Iss-3

Sequence Alignment and Phylogenetic Tree Construction of Malarial Parasites

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Sequence Alignment and Phylogenetic Tree Construction of Malarial Parasites

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