DNA Cryptography and Deep Learning using Genetic Algorithm with NW algorithm for Key Generation

Cryptography is not only a science of applying complex mathematics and logic to design strong methods to hide data called as encryption, but also to retrieve the original data back, called decryption. The purpose of cryptography is to transmit a message between a sender and receiver such that an eavesdropper is unable to comprehend it. To accomplish this, not only we need a strong algorithm, but a strong key and a strong concept for encryption and decryption process. We have introduced a concept of DNA Deep Learning Cryptography which is defined as a technique of concealing data in terms of DNA sequence and deep learning. In the cryptographic technique, each alphabet of a letter is converted into a different combination of the four bases, namely; Adenine (A), Cytosine (C), Guanine (G) and Thymine (T), which make up the human deoxyribonucleic acid (DNA). Actual implementations with the DNA don’t exceed laboratory level and are expensive. To bring DNA computing on a digital level, easy and effective algorithms are proposed in this paper. In proposed work we have introduced firstly, a method and its implementation for key generation based on the theory of natural selection using Genetic Algorithm with Needleman-Wunsch (NW) algorithm and Secondly, a method for implementation of encryption and decryption based on DNA computing using biological operations Transcription, Translation, DNA Sequencing and Deep Learning.</p

Manual on application of molecular tools in aquaculture and inland fisheries management. Part 2. Laboratory protocols and data analysis

The aim of this manual is to provide a comprehensive practical tool for the generation and analysis of genetic data for subsequent application in aquatic resources management in relation to genetic stock identification in inland fisheries and aquaculture. The material only covers general background on genetics in relation to aquaculture and fisheries resource management, the techniques and relevant methods of data analysis that are commonly used to address questions relating to genetic resource characterisation and population genetic analyses. No attempt is made to include applications of genetic improvement techniques e.g. selective breeding or producing genetically modified organisms (GMOs). The manual includes two ‘stand-alone’ parts, of which this is the second volume: Part 1 – Conceptual basis of population genetic approaches: will provide a basic foundation on genetics in general, and concepts of population genetics. Issues on the choices of molecular markers and project design are also discussed. Part 2 – Laboratory protocols, data management and analysis: will provide step-by-step protocols of the most commonly used molecular genetic techniques utilised in population genetics and systematic studies. In addition, a brief discussion and explanation of how these data are managed and analysed is also included. This manual is expected to enable NACA member country personnel to be trained to undertake molecular genetic studies in their own institutions, and as such is aimed at middle and higher level technical grades. The manual can also provide useful teaching material for specialised advanced level university courses in the region and postgraduate students. The manual has gone through two development/improvement stages. The initial material was tested at a regional workshop and at the second stage feedback from participants was used to improve the contents

DNA digital data storage and retrieval using algebraic codes

DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base pairs should be avoided to prevent the formation of a secondary structure in DNA strands. We overcome these challenges by selecting appropriate group homomorphisms. For storing and retrieving information in DNA strings we use kernel code and the Varshamov-Tenengolts algorithm. The Varshamov-Tenengolts algorithm corrects single indel errors. Additionally, we construct codes of any desired length (n) while calculating its reverse complement distance based on the value of n.Comment: 7 pages, 3 figure

Hybrid optimizer for expeditious modeling of virtual urban environments

Tese de mestrado. Engenharia Informática. Faculdade de Engenharia. Universidade do Porto. 200

Nanopore MinION -sekvensointimenetelmä pitkille DNA-fragmenteille : menetelmän testaus ja arviointi

Oxford Nanopore MinION on uusi kolmannen sukupolven sekvensointilaite, jolla on monia erityispirteitä. MinION:n käyttämä nanopore -sekvensointimenetelmä perustuu havaittavissa olevien jännitevirtausten muutosten mittaamiseen DNA- tai RNA-juosteiden kulkeutuessa nanokokoisten huokosten eli porejen kautta membraanin läpi. Menetelmä mahdollistaa juosteiden suoran sekvensoimisen ilman välireaktioita. Uniikista sekvensointitavastaan johtuen MinION -laitteen tyyppiominaisuudet ovat hyvin erilaiset kuin laajemmin käytössä olevilla sekvensointilaitteilla. Myös MinION -laitteen poikkeuksellisen pieni koko auttaa sitä entisestään erottumaan kilpailijoistaan. Nanopore-pohjainen sekvensointiteknologia ja MinION ovat kuitenkin olleet kaupallisesti saatavilla vasta lyhyen aikaa. Siksi menetelmä on vielä suurelta osin standardisoimaton ja sen sovellettavuutta tutkimuskäytössä ei pystytä vielä tarkasti arvioimaan. Tässä pro gradu -työssä kuvataan MinION -sekvensoinnin käyttöönottoa sekä arvioidaan sen suorituskykyä. Työn käytännön tutkimus aloitettiin jo ennen laitteen kaupallista julkaisua markkinoille osana erillistä ennakkotestausohjelmaa nimeltä MinION Access Programme (MAP) ja se jatkui katkeamatta myös MinION:n kaupallisen lanseerauksen jälkeen. Tutkimuksessa sekvensoitiin sekä E.coli-kasvatuksesta että ihmisverestä eristettyjä gDNA-näytteitä. Tuloksena saadut sekvenssit oli pääosin mahdollista linjata referenssigenomeihin. Sekvensointi- ja analyysivaiheiden optimoinnin jälkeen yhdellä sirulla pystyttiin tuottamaan tarpeeksi sekvenssidataa kattamaan E.coli-genomi kokonaisuudessaan keskimääräisellä 180x lukusyvyydellä. Tutkimuksessa arvioitiin MinION:n suorituskykyä tavoitteena arvioida, sopiiko menetelmä ihmisgenomin hankalasti sekvensoitavien alueiden luotettavaan tutkimiseen. Lisäksi testattiin mahdollisuutta täydentää sekvensointimenetelmää erillisellä protokollalla kohdennetun sekvensoinnin toteuttamiseksi. Tutkimuksen tulokset osoittavat, että MinION – menetelmää voidaan käyttää pitkien ja linjattavissa olevien sekvenssien tuottamiseen. Sirujen sekvensointikapasiteetti ja sekvenssien laatu kuitenkin rajoittavat menetelmän käytettävyyttä monimutkaisempien genomien tutkimuksessa. Kohdennusprotokollan ja muiden täydentävien menetelmien liittäminen osaksi sekvensointiprosessia voi auttaa näiden puutteiden ratkaisemisessa, mutta tällaisten laajennusprotokollien käyttöönotto saattaa olla haasteellista.The Oxford Nanopore MinION is a third generation sequencer utilizing nanopore sequencing technology. The nanopore sequencing method allows sequencing of either DNA or RNA strands as they pass through the membrane-embedded nanopores. By measuring the corresponding fluctuations in the ion flow passing through the nanopore the passing strands can be sequenced directly without additional second-hand reactions or measurements. The MinION sequencing has very distinctly different characteristics compared to the market leaders of the sequencing field. The small form factor of the device further helps it to separate itself from the other alternatives. However, the technology has only been on the market for a very short time and thus very little golden standards regarding its capabilities or usage have been established. This thesis describes our experiences testing the capabilities of the MinION sequencer both before its commercial release as a part of a special early access program, as well as our continued experiments with the device following its commercial launch. The main results of this study include successfully sequencing and aligning E.coli and human gDNA samples to their respective reference genomes. Using our sequencing and analysis pipeline specifically tuned to the MinION we were able to sequence the entire E.coli genome on a single MinION flow cell with an average depth of around 180. Over the course of the thesis project the MinION sequencing protocol was evaluated and optimized in order to determine whether it has the potential to achieve our ultimate goal of reliably sequencing the previously inaccessible genomic regions of the human genome. The possibility of augmenting the sequencing protocol by adding the pre-sequencing target enrichment was also explored. Ultimately we were able to confirm that the MinION sequencer can be used to sequence long DNA fragments from a multitude of sample types. The majority of the produced reads could successfully be aligned against a reference genome. However, the limited yield and sequencing quality of a single experiment does limit the applicability of the method for more complicated genomic studies. These issues can be addressed with various techniques, chiefly target enrichment, but adapting such methods into the sequencing pipeline has its own challenges

High levels of population genetic differentiation in the American crocodile (Crocodylus acutus)

The American crocodile (Crocodylus acutus) is a widely distributed species across coastal and brackish areas of the Neotropical region of the Americas and the Greater Antilles. Available information on patterns of genetic differentiation in C. acutus shows a complex structuring influenced by interspecific interactions (mainly hybridization) and anthropogenic actions (mostly historical hunting, recent poaching, habitat loss and fragmentation, and unintentional translocation of individuals). In this study, we used data on mitochondrial DNA control region and 11 nuclear polymorphic microsatellite loci to assess the degree of population structure of C. acutus in South America, North America, Central America and the Greater Antilles. We used traditional genetic differentiation indices, Bayesian clustering and multivariate methods to create a more comprehensive picture of the genetic relationships within the species across its range. Analyses of mtDNA and microsatellite loci show evidence of a strong population genetic structure in the American crocodile, with unique populations in each sampling locality. Our results support previous findings showing large degrees of genetic differentiation between the continental and the Greater Antillean C. acutus. We report three new haplotypes unique to Venezuela, which are considerably less distant from the Central and North American haplotypes than to the Greater Antillean ones. Our findings reveal genetic population differentiation between Cuban and Jamaican C. acutus and offer the first evidence of strong genetic differentiation among the populations of Greater Antillean C. acutus