Top PDF Fuzzy-based Spectral Alignment for Correcting DNA Sequence from Next Generation Sequencer

Fuzzy-based Spectral Alignment for Correcting DNA Sequence from Next Generation Sequencer

Fuzzy-based Spectral Alignment for Correcting DNA Sequence from Next Generation Sequencer

Deciding which tuples are included into solid tuples or weak tuples is not enough by using only multiplicity because sometimes tuples that have low qualities can be classified as solid tuples. Thus, in this research, we combined the parameter of multiplicity and base quality score of each reads to handle the problem of correcting sequencing errors. In this study, we proposed to represent the multiplicity and the base quality score in term of fuzzy. The fuzzy approaches were actually has been proven successful in solving the problem in the real world, such as integrating production capability and load balancing during scheduling activity [11], classify likelihoods of purchasing health insurance [12], predict the cases of Failed Back Surgery Syndrome (FBSS) [13], classify and analyze Microarray Gene data by using data mining and fuzzy logic [14], analyze the relationships between genes and help decipher a genetic network [15], building lighting system based on fuzzy logic scheme to automate fluorescent lamps in order to achieve illumination according to Indonesian National Standard (SNI) [16], and handle ambiguity perceived symptoms the patient and the certainty factor method to handle the relationship between the symptoms of the disease [17].
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Metode Spectral Alignment Berbasis Fuzzy Untuk Pengoreksian Sequence Dna Dari Next Generation Sequencer

Metode Spectral Alignment Berbasis Fuzzy Untuk Pengoreksian Sequence Dna Dari Next Generation Sequencer

Dalam ilmu biologi dan kesehatan, deoxyribonucleic acid (DNA) merupakan makromolekul yang sangat penting. DNA berfungsi untuk menyimpan semua informasi tentang genetika dari makhuk hidup (Bryce & Pacini 1998). Proses sequencing diperlukan untuk mengetahui urutan DNA. Dengan kata lain, sequencing merupakan suatu proses pembacaan urutan DNA. Hasil yang diperoleh berupa sekuen DNA yang dapat digunakan untuk menemukan gen, menemukan daerah yang memiliki kode untuk suatu protein yang spesifik, dan dapat membandingkan homologous DNA sequences dari organisme yang berbeda (Rogers 2011). Proses sequencing saat ini juga diterapkan untuk berbagai sampel tumor dalam upaya untuk mengidentifikasi mutasi terkait dengan kanker (Chong et al. 2012).
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IDENTIFIKASI VIRUS AVIAN INFLUENZA SUB TIPE H3 BERDASARKAN GEN PENYANDI PROTEIN HA MENGGUNAKAN NEXT GENERATION SEQUENCER PENELITIAN EKSPERIMENTAL LABORATORIS Repository - UNAIR REPOSITORY

IDENTIFIKASI VIRUS AVIAN INFLUENZA SUB TIPE H3 BERDASARKAN GEN PENYANDI PROTEIN HA MENGGUNAKAN NEXT GENERATION SEQUENCER PENELITIAN EKSPERIMENTAL LABORATORIS Repository - UNAIR REPOSITORY

Samples used in this study were local isolated samples in 2013 that were obtained from Influenza, CRC-ERID, ITD, Airlangga University. The samples grown in chicken eggs sprout to increase the number of viruses. Once harvested will be followed by HA test to determine isolates that have the ability to agglutinate chicken red blood cells. Isolates were then carried out to determine type A subtype H5 Influenza virus using POCube and One Step Real Time RT- PCR. Further detection of influenza virus sub-type is used NGS. Sequence results were analyzed using CLC Workbench ver. 8.0.2 to determine the HA protein- coding genes. Homology, alignment and amino acids analysis of the gene encoding the HA cleavage site using Genetyx ver. 12. References for the pathogenicity analysis based on the HA cleavage site used H5N1 1997 Guangdong goose 3 (AF364334) and the 2007 H5N1 Indonesia CDC1046 (CY019408) as a reference for the High Pathogenic, while for 2010 H3N6 Low Pathogenic used Jiangsu 4 (KC261677) and H3N6 2009 Guangxi 020P (KM186122).
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Spectral-based Features Ranking for Gamelan Instruments Identification using Filter Techniques

Spectral-based Features Ranking for Gamelan Instruments Identification using Filter Techniques

Feature selection is a process of finding an optimal feature subset, removes irrelevant or redundant feature. Feature selection is one of the important steps in machine learning especially for recognition tasks. The performance of recognition algorithms are usually dependent on the quality of the feature set. If the feature set contains redundant or irrelevant features, the algorithm may produce a less accurate or a less recognition rate. The feature selection problem has been studied by the statistics and machine learning communities for many years [1-4]. The feature selection algorithms can be categorized as filter, wrapper, and embedded methods based on the criterion functions. Filter methods uses statistical properties for evaluating feature subsets. The advantages of filters methods are fast and efficient to process high dimensional datasets, however filters approach do not consider the feature dependencies. Wrapper methods use a learning algorithm for evaluating the selected feature subsets. Embedded methods are similar to wrapper methods, but less computationally expensive and considering feature dependencies [5]. Feature extraction can be viewed as finding a subset of raw data while reducing the dimensionality.
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DESIGN OF POTENTIAL CELLULASE PRIMER USING MULTIPLE SEQUENCE ALIGNMENT METHOD

DESIGN OF POTENTIAL CELLULASE PRIMER USING MULTIPLE SEQUENCE ALIGNMENT METHOD

Progressive alignment methods use the dynamic programming method to build a multiple sequence alignment starting with the most related sequences and then progressively adding less related sequences or groups of sequences to the initial alignment [15-16]. Relationships among the sequences are modeled by an evolutionary tree where the outer branches or leaves are the sequences. The tree is based on pairwise comparisons of the sequences using one of the phylogenetic methods [17]. Progressive alignment algorithm is as follows:
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Multiple Sequence Alignment Menggunakan Nature-Inspired Metaheuristic Algorithms - ITS Repository

Multiple Sequence Alignment Menggunakan Nature-Inspired Metaheuristic Algorithms - ITS Repository

Multiple sequence alignment adalah proses dasar yang sering dibutuhkan dalam mengolah beberapa sequence yang berhubungan dengan bioinformatika. Apabila multiple sequence alignment telah selesai dikerjakan, maka dapat dilakukan analisis-analisis lain yang lebih jauh, seperti analisis filogenetik atau prediksi struktur protein. Banyaknya kegunaan dari multiple sequence alignment mengakibatkannya menjadi salah satu permasalahan yang banyak diteliti. Banyak algoritma-algoritma metaheuristic yang berdasar pada kejadian-kejadian alami, yang biasa disebut dengan nature-inspired metaheuristic algorithms. Beberapa algoritma baru dalam nature-inspired metaheuristic algorithms yang dianggap cukup efisien antara lain adalah firefly algorithm, cuckoo search, dan flower pollination algorithm. Dalam penelitian ini dipaparkan modified Needleman- Wunsch alignment. Didapatkan hasil bahwa modified Needleman-Wunsch alignment adalah metode yang cukup bagus. Modified Needleman-Wunsch alignment tersebut digunakan untuk membentuk solusi awal dari firefly algorithm, cuckoo search, dan flower pollination algorithm. Didapatkan hasil bahwa firefly algorithm, cuckoo search, dan flower pollination algorithm dapat menghasilkan solusi-solusi baru yang lebih baik. Secara keseluruhan, firefly algorithm adalah algoritma yang terbaik dari tiga algoritma tersebut dalam segi skor alignment, namun membutuhkan waktu komputasi yang lebih besar.
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AKTIVITAS PUBLIC RELATIONS DALAM UPAYA PENCITRAAN KAFE LIQUID NEXT GENERATION

AKTIVITAS PUBLIC RELATIONS DALAM UPAYA PENCITRAAN KAFE LIQUID NEXT GENERATION

Citra negative semacam ini bila dibiarkan begitu saja akan berdampak pada eksistensi Kafe Liquid Next Generation itu sendiri, dimana tingkat kepercayaan publik akan hilang sehingga omzet penghasilan perusahaan akan menurun dan tidak menutup kemungkinan akan mengalami kebangkrutan. Oleh karena itu diperlukan strategi yang tepat untuk menangani persoalan image suatu perusahaan. Bagaimanapun juga sebagai perusahaan terutama perusahaan komersial yang pada dasarnya mempunyai tujuan utama mendapatkan laba sebanyak – banyaknya, sebuah perusahaan tidak boleh mengabaikan kepentingan publiknya. Perusahaan tidak hanya sebatas memberikan produk berupa barang atau jasa yang berkualitas dengan harga murah. Untuk itu timbal baliknya perusahaan harus menjalin hubungan yang harmonis serta memberikan pelayanan yang baik kepada masyarakat untuk meningkatkan tingkat kepercayaan publiknya. Hal tersebut merupakan suatu tantangan dan tujuan bagi humas untuk mengatasi anggapan negatif sebagian masyarakat. Humas merupakan seseorang yang diharapkan dapat mengatasi masalah yang menyangkut tentang perusahaan seperti Kafe Liquid Next Generation.
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KONSUMSI DAYA PADA SPLITTER UNTUK JARINGAN OPTICAL NEXT GENERATION

KONSUMSI DAYA PADA SPLITTER UNTUK JARINGAN OPTICAL NEXT GENERATION

The evolution of Gigabit Passive Optical Network (GPON) technology to Next Generation Passive Optical Network stage 2 (NGPON2) is a step in delivering better services that deliver bandwidth and quality of service (QOS) for high-speed best-effort connectivity services with more split ratio and further range. In this research will design and simulate Bidirectional NGPON2 network with TWDM technique which has total bitrate 40 Gbps for downstream and 10 Gbps for upstream by using 3 stage combination passive splitter at 30 km distance. Approach to get results using power link budget calculations, BER and Q factors then refers to the ITU-T standard.
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Test Case Generator for testing Sequence Diagram Based Applications

Test Case Generator for testing Sequence Diagram Based Applications

Terdapat delapan diagram UML model yang dapat digunakan untuk memodelkan sebuah perancangan model. Dari kedelapan diagram tersebut yang dapat digunakan untuk membangkitkan kasus uji misalnya sequence diagram. Sequence diagram dapat digunakan untuk melihat perilaku sistem. Keunggulan dari sequence diagram dibandingkan dengan diagram model lain untuk membangkitkan kasus uji adalah sequence diagram menggambarkan interaksi behavior sistem dan menggambarkan interaksi antar objek dalam sebuah urutan waktu. Pembangkitan kasus uji yang dilakukan dengan sequence diagram tentunya akan mempercepat pembuatan sebuah kasus uji. Kasus uji yang biasanya dihasilkan setelah tahap coding selesai, kini dapat dihasilkan pada saat tahap design. Sehingga kasus uji dapat langsung digunakan untuk menguji aplikasi saat tahap coding selesai. Oleh karena itu pada tugas akhir mengangkat judul “Pembangkitan Kasus Uji untuk Pengujian Aplikasi Berbasis Sequence Diagram ” yang bertujuan untuk menghasilkan sekumpulan kasus uji berdasarkan sequence diagram yang dapat diperoleh pada saat tahap design. Kasus uji yang telah dihasilkan oleh tools kemudian diterapkan untuk pengujian aplikasi, pengujian dengan kasus uji yang telah dihasilkan oleh tools dilakukan dengan automatic testing dengan menggunakan Selenium WebDriver.
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Springer Next Generation Intelligent Optical Networks From Access To Backbone Dec 2007 ISBN 0387717552 pdf

Springer Next Generation Intelligent Optical Networks From Access To Backbone Dec 2007 ISBN 0387717552 pdf

Wavelength switching is simple in the sense that a single (or the same) wavelength connects two points across the network. This method is also known as “wavelength assignment” (WA). When the network is pre-provisioned to provide connectivity with the same wavelength for a long period, then this is termed static WA. This method provides a better wavelength efficiency but the efficiency depends on the number of wavelengths per fiber and also on the number of fibers in and out each node. Node provisioning is relatively easy and it can be achieved with centralized control (or man- agement) or with distributed control. Conversely, a path may be determined and the same wavelength may be assigned on a per call basis; this is known as dynamic WA. Static and dynamic wavelength assignment cannot warranty that there will always be the same wavelength available across the net- work. However, the wavelength assignment is greatly improved if wavelength converters are used in each node. In this case, a route is established by using different available wavelengths. In this case, the wavelength assignment with wavelength conversion has the highest efficiency. However, what is more important is the efficiency of traffic deliverability, which depends on the traffic utilization of each wavelength. For example, if the data rate on each wavelength is 10 Gbps, the question is, what is the effective data rate each wavelength transports? It is clear that a route may be established to transport end-user data, which is a fraction of 10 Gbps. This problem is not much different than the flow in a pipe. A pipe may connect two points but it does not warranty that it will always be full; think that a pipe is a wavelength.
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Komputasi Paralel Multiple Sequence Alignment menggunakan Message Passing Interface

Komputasi Paralel Multiple Sequence Alignment menggunakan Message Passing Interface

Evaluasi kinerja dari metode yang diusulkan dilakukan dengan menghitung speedup. Percobaan dilakukan dengan menggunakan data Glycine max-kromosom-9-BBI dengan jumlah 64 sekuen yang memiliki panjang seragam, yaitu 800 base pair (bp). Sekuens ini dihasilkan dengan cara memotong secara acak sekuen referensi dari Glycine max-kromosom-9-BBI yang bersumber dari national center for biotechnology information (NCBI). Hasil penelitian menunjukkan bahwa teknik yang diusulkan mampu menghasilkan speedup sebesar tiga kali, dengan menggunakan lima komputer. Selain itu, dapat ditarik kesimpulan bahwa peningkatan jumlah komputer akan meningkatkan speedup. Kata kunci : multiple sequence alignment, message passing interfaces, komputasi
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Next Generation Networks  Proceedings of CSI 2015 pdf  pdf

Next Generation Networks Proceedings of CSI 2015 pdf pdf

overhead information and thus decreasing the overall throughput of transmission. The automatic modulation technique alleviates this problem by offering the advantage of classifying the modulation parameters at receiver side automatically and aids in demodulating the signal. If the classifying algorithm does not consume much receiver processor power or increase latency in network, then the net gain is bandwidth saving. ITU Recommendation SM.1600-1 suggests manual and auto- matic methods of classifying modulation in these networks. Under automatic methods, autocorrelation techniques are proposed to detect periodic sequences, such as preamble or mid-amble, synchronization word or pilot codes, and training sequences embedded in signal. Cyclic autocorrelation can identify OFDM and OFDMA standard signals by detecting the periodicity embedded in signal. Advanced methods like Haar wavelet transform can automatically identify if there is some a priori information available for transmission parameters. However, these techniques can identify standard signals only that comply to specifications. There have been many other techniques developed to classify OFDM signals. In this paper, we focus to evolve method to classify Worldwide Interoperability for Microwave Access (WiMAX) IEEE 802.16d OFDM signal used on air interface using neural network.
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Penyusunan Overlap Graph menggunakan Suffix Tree pada DNA Sequence

Penyusunan Overlap Graph menggunakan Suffix Tree pada DNA Sequence

Konfigurasi MetaSim yang tersaji pada Gambar 3 terdapat beberapa parameter yang harus dipilih dan diisi, “Preset Name” diisi untuk memberikan nama dari konfigurasi itu sendiri, lalu “Number of Reads or Mate Pairs” yaitu jumlah fragmen yang ingin kita bangkitkan pada suatu DNA sequence . “Error Model” t erdiri atas 454, Empirical, Sanger dan Exact, untuk mendapatkan data sequence yang tidak memilik i kesalahan maka harus dipilih “Error Model” Exact. “DNA Clone Size Distribution Type” terdiri atas Uniform, Normal, dan Empirical, pada penelitian ini tipe distribusi yang dipilih yaitu Normal, s edangkan “Mean” yaitu panjang sequence setiap fragmennya, pe nelitian ini dipilih “Mean” dengan panjang 35 bp dan “Second Parame ter” dipilih 0 (nol). Konfigurasi ini menghasilkan fail yang berformat .mprf.
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Perancangan Next Generation OPAC Berbasis Library 2.0 Di STT Amanat Agung

Perancangan Next Generation OPAC Berbasis Library 2.0 Di STT Amanat Agung

Prototipe II Next Generation OPAC merupakan pengembangan dari Prototipe I Next Generation OPAC dengan menambahkan tiga fungsionalitas yang merupakan usulan dari pengguna. Ketiga fungsionalitas ini merupakan tugas-tugas yang dilakukan administrator untuk memperbaiki tampilan antarmuka prototipe. Perubahan pertama terjadi pada judul dan logo situs web yang lebih mencirikan identitas tempat penelitian dilakukan. Perubahan kedua adalah My Account berubah menjadi nama pengguna, jika pengguna log in pada sistem, sehingga lebih memberikan aspek personal bagi pengguna. Hal ketiga adalah penambahan tag cloud, yang menampilkan semua tag yang dimasukkan oleh pengguna.
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Quality-based Spatial/Spectral Image Transformation.

Quality-based Spatial/Spectral Image Transformation.

Compressing the image on the server side or within the GIS network is considered to be the ideal solution, where the images can be compressed to their smallest usable size; therefore the volume of data transmitted across the network is reduced [10]. The purpose of compressing an image is to reduce the bandwidth required and storage requirement, which in turn increase the usefulness of GIS services. During compression process, certain amount of image redundancy is reduced due to the transformation of the image matrix. Visual distortion in exchange for a fewer bandwidth and storage might considered tolerable to the human eyes [18]. Nevertheless, a certain error metric has been used to determine the image quality and possible usefulness of the reconstructed data in analysis, such as detection and classification.
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Mobile Peer to Peer Computing for Next Generation Distributed Environments  Advancing Conceptual and Algorithmic Applications pdf  pdf

Mobile Peer to Peer Computing for Next Generation Distributed Environments Advancing Conceptual and Algorithmic Applications pdf pdf

the number of duplicated and lost messages, but defined no other metrics to evaluate the system performance. (Podnar & Lovrek, 2004) proposed a mobility extension based on persistent messages that require the delivery of valid messages just after the activation of a new subscription in the systems. Each broker is responsible for storing the arrived messages in a persistent buffer and then forwards them to interested subscribers and neighboring brokers. The messages are deleted once their validity period expires. The broker also maintains a list of valid messages that have been delivered to subscribers and brokers. When a subscriber reconnects to the system, the broker activates its subscriptions and sends the valid buffered messages. The subscriber must provide a list of the previous consumed messages to avoid duplicate messages. This approach clearly creates extra traffic in the broker network, and increases broker memory consumption and processing time. In contrast, our approach reduces this overhead as it propagates only the subscriptions to the neigh- boring brokers and buffers messages only when subscribers become inactive/disconnected. The REBECA project (Zeidler & Fiege, 2003) relies on a reactive approach for supporting mobility. The last visited broker plays the role of a proxy subscriber. Whenever a subscriber reconnects to a new broker, it re-submits its subscriptions. The broker network finds the old broker by locating a broker at the junction of delivery paths to the new and old broker. It is straightforward to find a junction broker if the broker network uses simple routing, because each broker keeps entries about all active subscriptions. The notifications stored by the old broker are routed through the junction to reach the new broker, and then the subscriber. The authors do not justify why subscribers cannot maintain the information about the last visited broker. There are currently no results that evaluate the performance of the approach. The mobility extension in ELVIN (Sutton et al., 2001) is mainly based on a central caching proxy server that mediates between the original server
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Spectral dimensionality reduction based on intergrated bispectrum phase for hyperspectral image analysis.

Spectral dimensionality reduction based on intergrated bispectrum phase for hyperspectral image analysis.

In this paper, we propose a method to reduce spectral dimension based on the phase of integrated bispectrum. Based on the area size of the integrated bispectrum, the resulting phase can be split into a number of features. The resulting feature vectors are then used to represent the spectral of each pixel in the hyperspectral image. Because of the excellent information extracted by the bispectrum, the resulting feature has high discriminating power even with only single dimension data. The phase of the integrated bispectrum feature is tested on spectral classification and HSI segmentation.
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Migration from Gasoline to Gaseous Fuel for Small-scale Electricity Generation Systems

Migration from Gasoline to Gaseous Fuel for Small-scale Electricity Generation Systems

have combustion process cleanly. It has density of 1.779 Kg/m 3 at Standard Temperature and Pressure (STP), molecular weight of 44, ratio Stoich air/fuel is 15.7, and Lower Heat Value of 46.33 MJ/Kg. Besides, it can be stored at atmospheric pressure so there are no evaporative losses. Propane has a good volumetric energy content and road octane number of more than 100. The main advantage of using combustible gases as fuel compared to gasoline is a cleaner emitted gas after combustion, while the output power seemed similar. The LPG nowadays existing abundantly and inexpensively in the developing countries such as in Indonesia, wherein the transformation from using fossil fuel into gas has been encouraged by the government. Another combustible gas coulbe be produced from anaerobic digestion of organic compounds in wastewater or solid waste, from which the pollutant could harm the environment once they are casted out without further treatment. Therefore, using wastes as source of electrical generation system by converting them into biogas will bring two benefits: renewable energy source and environmental friendly technology.
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Pengkonstruksian Bidirected Overlap Graph Untuk Dna Sequence Assembly

Pengkonstruksian Bidirected Overlap Graph Untuk Dna Sequence Assembly

DNA sequencing technologies dapat digunakan untuk memecah gen bakteri menjadi jutaan potongan kecil yang disebut reads. Namun demikian, reads tersebut perlu disambung menjadi contigs agar dapat digunakan. Terdapat 2 metode untuk menyambungkan reads. Yang pertama dengan menggunakan overlap layout consensus (OLC) dan yang lainnya dengan menggunakan de Bruijn graph. Hal penting dalam metode OLC adalah bagian overlap dari masing- masing reads. Pada penelitian ini dikembangkan sebuah sistem untuk membuat bidirected overlap graph yang nantinya akan menghitung berapa jumlah reads yang saling overlap satu sama lain. Suffix array digunakan untuk menentukan fase/bagian overlap dari setiap reads dengan mengindeks setiap suffix dari reads. Waktu adalah parameter penting dalam DNA assembly karena DNA assembly membutuhkan banyak waktu. Untuk mengurangi waktu dilakukan perubahan dari masing-masing suffix dan prefix menjadi suatu nilai tertentu yang bersifat tunggal dan mencari overlap dengan membandingkan setiap reads. Cara ini memberikan dampak positif daripada perbandingan dengan menggunakan string. Perbandingan waktu yang diperlukan antara perbandingan angka dan perbandingan string cukup signifikan. Untuk 2000 dan 5000 reads, sistem dapat memberikan hasil 100% akurat untuk jumlah node dan edge.
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