CONTENTS:I. ABSTRACT II. INTRODUCTION III. EARLIER MEASURES IV.

NEWER APPROACHES a) b) c)
USING NEURAL NETWORKS USING CELLULAR AUTOMATA DISTRIBUTED DATABASES

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7 13 18

V. TWO STAGE CLASSIFIER VI. FUTURE WORKS VII. CONCLUSION VIII. REFERENCES
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PROTEIN CODING REGION IDENTIFICATION
Abstract:- Genes carry the instructions for making proteins that are found in a cell as a specific sequence of nucleotides in DNA molecules. These specific sequences of bases encode instructions on how to make protein. But the regions of gene that code for proteins may occupy only a small region of a sequence. The problem of gene recognition is to define an algorithm which takes as input DNA sequence and produces as output a feature table describing the location and structure of the patterns making up any genes present in the sequence. Identifying the coding region is of vital importance in understanding these genes. Here I have given certain pattern classifiers which will the test data set presented by fickett and tung to identify protein coding regions. Firstly we have considered some of the test data set using earlier measures for PCRI. We have described some of them not all Then we have proposed both Feed Forward connectivity and Backpropagation approach of neural networks for test data identification. We have found a highly accurate but space consuming CRM module. We have compared its results Then we propose cellular automata based pattern classifier to identify the coding region of a DNA sequence both in centralized and distributed databases. CA is simple efficient and produces more accurate classifier than that have previously been obtained for a range of different sequence lengths. And we have compared some of the older measures with FMACA based pattern classifier. At the end a genetic algorithm based two-stage pattern classifier was used to solve the PCRI. And although implementation was not done but we have found its effectiveness in various other data bases and suitable work can be done in this direction.

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Our objective is to define an algorithm which takes an input DNA sequence and produces an output a feature table describing the location and structure. There are two types of regions Coding and Non-coding. A protein coding gene basically found in a t -RNA It is any pattern in a DNA sequence It results in the generation of protein product through a process known as transcription.Protein Synthesis in a DNA 3|Page .N C N h t is P otein Coding egion dentifi tion? It is a technique to identify the coding (EXONS) and non coding (INTRONS) region in a protein coding base. Fig 1:.

It can be a good mechani m for genetic engineering.How to Develop an Algorithm 4|Page . 2. but for a systematic approach to building a comprehensive recognition algorithm one thing is still missing. the patterns at Intron junctions.. Possibilit exists of using computational procedures to anal l i i i t t i t i e raw base sequence information and to predict coding regions (as well as other signal regions) by the use of duplicate fragments. and then to build a combined algorithm that recogni es when all these component patterns occur in a pattern consistent with that present in a gene . 3. How to build an algorithm for PCRI? A natural overall approach to building gene recognition algorithms is to first construct component algorithms that recogni e the major features of genes: statistical bias in Exon sequence. namely an objective comparison and evaluation of the competing recognition techniques. etc. A great many ideas have been suggested for recognition of the components of genes.bje tives of PC :1. It i i . 4. Finding Protein coding regions these sequences biochemicall is time consuming and expensi e. enhancers. promoters. Fig 2:.

It contains an entry which gives longest contiguous subsequence that has all entries from s V. Position asymmetry measure: .A coding measure is a vector of measurements on a DNA sequence.It is the vector of 4096 dicodon frequencies of every possible dicodon where the dicodon counts are accumulated at sights whose starting point is multiple of 3.They are offset by 1& 2 and similar to dicodon measure III. i )/3 Asymmetry is defined as assymm(b) = ™i ( f( b .ARL R MEASURES:A.C. Measures for Protein Coding regions Identifications Definition:.The extent to which the nucleotide is distributed over the three codon positions.Training Set of Fickett And Tung DataBase 5|Page . Codon usage Measure :.It is simply the longest sequence of codons that do not contain a stop codon. Dicodon Measure:. Run Measure: .The Run feature is a vector of length 14 for each non trivial subset S = {A. According to Fickett and tung there are 21 coding measures I. IV. i ) . Hexamer-1 & 2 :. II.The codon usage feature is a vector of 64 codon frequencies. If f(b.i) is the frequency of base b over position I and (b) = ™i f( b.T}. Diamino Acid Usage measure :.(b) )2 VI. Open Reading Frame Measure:.G. Hyper plane Equation was used. VII.It is again a vector of the 440 amino acids frequency which are obtained by translating from nucleotide sequence to an amino acid string Fig 3:.

B. we define a window si e to be the width of the region over which each calculation is to be done 6|Page . Types of approaches Direct approach: Look for stretches that can be interpreted as protein using the genetic code Example: Open reading Frame measure Statistical approaches: Use other knowledge about likely coding regions Example: Dicodon usage Fig 4:-Open Reading Frame Measure Calculation Windows: Many sequence analyses require calculating some statistic over a long sequence looking for regions where the statistic is unusually high or low To do this.

Defi i i :. VI. combined with an internal function. Using neural networks:I.Name of this network is due to the direction of flow of the data. Processing:-The unit (also known as a neuron or node) is the main processing element of the neural network. So What we get a measure for learning.Unsupervised learning does not require a desired response (and therefore output data) to train and is concerned with discovering a common set of features across the input data in one class or pattern. Unsupervised learning:. Once trained.It is a number associated with a node which decreases or increases with each learning. Archi ecture :. II. Weights:.the task for the network is to relate the variables it receives in the input layer to some desired behaviour at the output layer by repeatedly presenting the examples to the network in a process known as training. It receives a set of input signals and. they consist of many units connected to each other by variable strength links layer and one µoutput¶ layer ± and are known as µperceptrons¶.NEWER APPROACHES:1. VIII. 7|Pa ge . Like the human brain.The errors incurred during learning are propagated back through the network. VII. converts the input signals to an output signal. This training is known as supervised learning IV.The simplest neural networks there are only two layers ± one µinput¶ III. Back Propagation:. V. Feed-Forward Approach:. But we can have multiple layer also. the neural network should be capable of predicting an output given a previously unseen set of inputs. Learning:.Neural networks were originally conceived as computational models of the way in which the human brain works.

i ) and the desired output (o) data to the network 3. 2. Calculate the output from the network using the expression: f (s) 4. Present the input data (1. (c) if output is 1 and should be 0 w (t + 1) = w (t) . w (t + 1) is the weight value at time t + 1 (i.e.Preceptron Learning Rule Where w (t) is the weight value at time t. . Adapt the weights: (a) if correct w (t + 1) = w (t). i2. (b) if output is 0 and should be 1 w (t + 1) = w (t) + i (t). Initiali e the network weights and unit thresholds to some small random values. .i (t). i3 .PERCEPTRON LE RNING RULE 1. ¡ ¡ ¡ ¡ ¡ ¡   ¡ ¡ Fig 1:. after updating) and f (s) is the function used to compute the output in the network 8|Page .

Calculate the output from the network using the expression f (s) ] for each layer in the network. 4. . The output from the final layer is the vector of output values. o is the actual output c is a constant used in the sigmoid function. Adapt the weights. 3. i2. i3 . Initiali e the thresholds and weights. The sum shown for hidden layers is over the k nodes in the layer above the current layer for which the pj will already have been computed Fig 6:. i ) and the desired output (o) data to the network. . Present the input data (i1. 2.Backpropagation:1.BackPropagation 9|Page ¢ . starting from the output layer and moving backwards using the equation Wij (t + 1) = wij (t) + pjopj d is the desired output.

Feed Forward Connectivity Fig 1:. III.Protein Synthesis in a DNA Fig 1:.s sixsi Where si represents the probability of codon s at position i p (T {Xi})=1/(1 + exp(™sTsNs + )) Ts = log ( qs + ps ) And = log (p (f)/p (t)) Fig 7:. Given a collection of examples labeled true or false for exons it is true for introns it is false II.Protein Synthesis in a DNA 10 | P a g e .Feed Forward Connectivity:I. We can employ a supervised Neural Network by using Bayes theorem p(T {Xi}) = p({Xi} T)p(T)/{p({Xi} T)p(T)+p({Xi} F)p(F)} Here P(t) and p(f) are the priori probabilities of the true class and false class. Assuming that individual codon positions are independent of the codons p({Xi} T)=šI.

CRM means Coding Recognition Module.0 and 1. This network is consisting of 7 input nodes . In the following table we will see that it is a very accurate algorithm Fig 10:. A back propagation neural net was created to integrate the output from the 7 sensors Algorithms.0 are then evaluated. and an output node. To determine the likely hood of a given sequence position a program written in C language is used which calculates the sensors Values for a 99 base sequence and the sensor signals between 0.CRM Based Approach:1. 6. 2 Hidden layers of 14 and 5 nodes . 3. 5. 2. 4.Using A CRM Module 11 | P a g e . The Coding Module is used to find exons or parts of exons that encode protein.

12 | P a g e .we see that our classifier almost gives a 99% accuracy.Fig 11:.Table showing a Database comparison for CRM NOTE:.

FMACA:‡ A FMACA is a special class of FCA that can efficiently model an associative memory to perform pattern recognition/classification task ‡ Its state transition behaviour consists of multiple components . Fig 12:. as noted in is an inverted tree. the next state qi(t+1) of a cell is assumed to be dependent only on itself and on its two neighbours (left and right). In a 3-neighborhood dependency. Using Cellular Automata:A Cellular Automaton (CA) can be viewed as an autonomous finite state machine (FSM) consisting of a number of cells. The global evolution results from synchronous application of the local rule to all cells of the array. ‡ A cycle in a component is referred to as an attractor. Each cell of the array assumes a state qi. qi(t) .2. and is denoted as qi(t+1)=f(qi-1(t) . ‡ The transient states finally settles down to one of the attractor basins after passing through a lot of intermediate states.State diagram of 3 cell 3 state FMACA 13 | P a g e .1] (fuzzy states) and changes its state according to a local evolution function on its own state and states of its two neighbours. qi+1(t) ) Fuzzy Cellular Automata:An elementary FCA is a linear array of cells which evolves in time. ‡ Each component. a rational value in the interval [0. each rooted on a cyclic state.

We show the algorithmic approach on building a tree classifier. Step 2. The elements of the training set S get distributed into k attractor basins/nodes.FMACA BASED K-means clustering Algorithm:Algorithm 1:Step 1. 14 | P a g e . Let S/ be the set of elements in an attractor basin. Step 3. Otherwise if S/ belongs to more than one class. Stop. all patterns of S/ are covered by an attractor basin/node belonging to only one particular class).e. Step 5. FMACA with k attractor basins is generated. then repeat the steps 1 to 4. Step 4. then mark it as a leaf node and label that attractor basin/node as that class. If S/ belongs to any one particular class (i.

Thus good implementation must be the focus. 2. T}. C. Small tree height leading to low retrieval time. Time complexity is O(n) By using Dependency Vector scheme 15 | P a g e . We have followed this procedure in our study and we have used the benchmark human dna database developed fickett and tung. An important issue in applying FMACA works to DNA sequence classification is how to encode DNA sequences as the input of the FMACA based tree structure classifier. Low error rate leading to maximum classification accuracy. The goal is to identify whether the entirely all-coding or all-non coding. From a one dimensional point of view a DNA sequence contain characters from a 4-letter base pair S = {A. Errors and other Benchmarks:The objective function (which is to be minimized) is the sums of squares distances of each DNA sequence and its assigned cluster centres. Less number of nodes leading to low memory overhead 3. SSdistances =™ x-C(x)2] where C(x) is the mean of the cluster that DNA position x is assigned to Minimizing the SSdistances is equivalent to minimizing the Mean Squared Error (MSE) Wrong to state that lesser MSE means better classifications The basic criteria for FMACA tree design are: 1. G.Implementation:For using a FMACA based classifier we need a limited window for eg 100 base pairs which can be used for standard experimental observations and it computes the features of that window alone.

Here we have compared with some of the other measures and found out that our FMACA based classifier is indeed a very accurate classifier. We have shown that in the graphs below. And also takes very less memory overhead and retrieval time. 16 | P a g e .

Fig 12:.FMACA INTERFACE 17 | P a g e .

18 | P a g e . ISSUES IN DISTRIBUTED DATABASES ` The aggregation of the base classifiers ` The communication cost from different local data sources to the central location where final classification is performed. ` Results derived out of base classifiers are next combined at central location to enhance the classification accuracy of predictive models. ` It should have high throughput with less storage requirements ` Volume of data transferred from each local to central site should be minimum ` Aggregation of base classifiers must induce globally meaningful knowledge.DISTRIBUTED DATABASES ` Distributed classifiers work in ensemble learning approach ` Multiple classifiers as base classifiers at different data sources. ` the base classifier at each local site must have high classification accuracy ` it must be scalable to handle disk resident datasets.

We have shown here algorithmic approach for distributed database PCRI 19 | P a g e .

Experimental observation 1. or mixed. with shorter pieces at the ends discarded. The FMACA based base classifiers (BCi s) are next collected in the centralized location where predictive accuracy is tested with the test set. Comparison: All the attributes in a dataset are normalized to facilitate FMACA learning. the possible value range of an attribute attri is (attrvali. There are 21 coding measures. Suppose. For Distributed Datasets: Total training set is equally distributed to each local site and then same scheme is employed at each local site to synthesize the FMACA. 2. The dataset also includes the reverse complement of every sequence. The tree then classifies the Test Set. 4. a coding measure is a vector of measurements on a DNA subsequence. The benchmark human data include three different datasets. non-overlapping human DNA sequences of length 54 have been extracted from all human sequences. then the normalized value of attrvalij i £ 20 | P a g e . For the first dataset. Every sequence is labeled according to whether it is entirely coding. They have surveyed and compared it. 3. and the mixed sequences are discarded.min. For Centralized Datasets: There is use of a training set exclusively to construct a FMACA tree based structured pattern classifier. entirely non-coding. which makes the problem of identifying coding regions somewhat harder. attrvalj. This means that one-half of the data is guaranteed to be from the non-sense strand of the DNA.max). Coding Measure: Typically. and the real value that class element j takes at attri is attrvalij. The predictive accuracy of the proposed scheme is evaluated through the majority voting scheme.

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We see as in below GA employed will significantly decrease the memory overhead 22 | P a g e .

FUTURE WORKS 1. ADVANTAGES 1. Use of SVM {Support Vector Machines}. 2. Can be used to genetically build protein Which can ensure higher immunity 3. Use of NNt Tree classification For MLP(multi layer perceptron) for better 4. Can be used successfully to locate a cancerous protein coding region 2. Use of autoregressive modelling approach for introducing better Protein coding region identification. Use of GA in FMACA classifiers 3.CANCER Treatment by Knowing The protein Code 23 | P a g e . Can be used to distinguish between different kinds of genes. Fig 13:.

7. ³Fuzzy Cellular Automata for Modeling Pattern Classifier´. in Proc. April 2005. vol. "Locating protein-coding regions in human dna sequences by a multiple sensor-neural network approach.. pp. 1991 P." Physica D. vol. Fuzzy cellular automata and their chaotic behavior. S. Mauri.. It is not far when our dream of becoming immortal and space travellers will come true. A study of fuzzy and many-valued logics in cellular automata. Sci. 13. Santoro (1993). vol. 10. P Pal Choudhary ³Cellular Automata in protein coding Region Identification ³ 9proceedings of ICISIP-2005 24 | P a g e . ³Basins of Attraction of Cellular Automata Based Associative Memory and its Rule Space´ Pradipta Maji. Maji and P. A New Kind of Science (2002). Sumanta Das. pp. Flocchini. vol. P. 12. 6." Nucleic Acids Res. vol. 1992. "Recognition of protein coding regions in dna sequences. Pradipta Maji and P. Chandrama Shaw. 691-702. Champaign. "Fuzzy Cellular Automata For Modeling Pattern Classifier. E88-D. Mural. 4. 16. REFERENCES:1. Wolfram Media. S. ´On The Relationship Between Boolean and Fuzzy Cellular Automata´ Pradipta Maji and P. Sirotkin. Acad. Heather Betel and Paola Flocchini. Santoro. A. 2000. 20. Fickett. pp. Thereby a lot of new opportunities emerge. 471-479. 15. and K. Mingarelli. 11. pp. 10." J.Pal Chaudhuri. Flocchini. "Assessment of protein coding measures." Nucleic Acids Res. G. 5303-5318. Sikdar and P. 226. A. R. 1285-1289. P. IEICE Volume 4. Natl. "Determination of eucaryotic protein coding regions using neural networks and information theory. Hawaii. 5.Pal Chaudhuri. Il. Biplab K. G. Lapedes. Uberbacher and R. F. P. Niloy Ganguly. "Convergence and Aperiodicity in Fuzzy Cellular Automata: Revisiting Rule 90. J. pp. 1992. 88. Samik Barua. 8. 14. J." Proc. Mol. 1126111265. E." IEICE Transactions on Information and Systems. and N. Geurts. 3. ³ ³Theory and Application of Cellular Automata for Pattern Classification´ Pradipta Maji and P. Cattaneo..Pal Chaudhuri. Farber. Angelo B. USA. Fickett and C. and N.Pal Chaudhuri.. Wolfram. Biol. Mingarelli(2007). 1982. 2. International Symposium on Nonlinear Theory and its Applications. ³Fuzzy Cellular Automata Based Associative Memory for Pattern Recognition´ Pradipta Maji and Chandra Das . 9. Chaudhuri. 6441-6450. Tung. Knowledge Discovery in Distributed Biological Datasets Using Fuzzy Cellular Automata Pradipta Maji.CONCLUSION:So hereby conclude that by using efficient PCRI we can successfully make corrections to faulty genes.

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