Parallel String Matching with Multi Core Processors-A Comparative Study for Gene Sequences

The increase in huge amount of data is seen clearly in present days because of requirement for storing more information. To extract certain data from this large database is a very difficult task, including text processing, information retrieval, text mining, pattern recognition and DNA sequencing. So we need concurrent events and high performance computing models for extracting the data. This will create a challenge to the researchers. One of the solutions is parallel algorithms for string matching on computing models. In this we implemented parallel string matching with JAVA Multi threading with multi core processing, and performed a comparative study on Knuth Morris Pratt, Boyer Moore and Brute force string matching algorithms. For testing our system we take a gene sequence which consists of lacks of records. From the test results it is shown that the multicore processing is better compared to lower versions. Finally this proposed parallel string matching with multicore processing is better compared to other sequential approaches

Patterns of visual adaptation in tropical mimetic butterflies

Species diversity within an ecosystem can be supported by favouring microhabitat specialisation. In complex habitats, like tropical rainforests, spatial and temporal segregation across microhabitats can expose species to distinct sensory realms. For many animals, visual systems serve as the primary conduit for perceiving biologically relevant sensory information, and the structural and functional variety of eyes and sensory brain regions reflects their critical role in diverse animal behaviours. However, little is known of their role in mediating niche segregation across subtle ecological scales, particularly in terrestrial environments. I explore the role of microhabitat partitioning in driving predictable patterns of adaptive visual system evolution within two diverse radiations of mimetic Neotropical butterfly, the Heliconius and Ithomiini. By taking a comparative approach, I investigate whether dual patterns of habitat divergence and convergence is manifested in the visual system at the perceptual, processing, and molecular level. I find extensive evidence of heritable, habitat-associated visual system variation, particularly for neural processing structures, hinting at the evolutionary lability of these systems to rapidly accommodate local adaptations to visual ecologies. My research also empirically demonstrates, for the first time, how variation in forest structure can give rise to distinct photic environments, highlighting the role of spectral variation as a major driver of adaptive community assemblage within a terrestrial forest radiation. In addition, evidence of visual morphological convergence offers a mechanistic insight into the evolvability of visual adaptations when confronted with similar ecological challenges, shedding light on their significance in promoting ecological diversification and speciation

Emerging model spedies driven by transciptomics

This work is focused on 'emerging model species', i.e. question-driven model species which have sufficient molecular resources to investigate a specific phenomenon in molecular biology, developmental biology, molecular ecology and evolution or related molecular fields. This thesis shows how transcriptomic data can be generated, analyzed, and used to investigate such phenomena of interest even in species lacking a reference genome. The initial ButterflyBase resource has proven to be useful to researchers of species without a reference genome but is limited to the Lepidoptera and supports only the older Sanger sequencing technologies. Thanks to Next Generation Sequencing, transcriptome sequencing is more cost effective but the bottleneck of transcriptomic projects is now the bioinformatic analysis and data mining/dissemination. Therefore, this work continues with presenting novel and innovative approaches which effectively overcome this bottleneck. The est2assembly software produces deeply annotated reference transcriptomes stored in the Chado database. The Drupal Bioinformatic Server Framework and genes4all provide species-neutral and an innovative approach in building standardized online databases and associated web services. All public insect mRNA data were analyzed with est2assembly and genes4all to produce the InsectaCentral. With InsectaCentral, a powerful resource is now available to assist molecular biology in any question-driven model insect species. The software presented here was developed according to specifications of the General Model Organism Database (GMOD) community. All software specifications are species-neutral and can be seamlessly deployed to assist any research community. Further through a case studies chapter, it becomes apparent that the transcriptomic approach is more cost-effective than a genomic approach and therefore sequence-driven evolutionary biology will benefit faster with this field

Focus: A Graph Approach for Data-Mining and Domain-Specific Assembly of Next Generation Sequencing Data

Next Generation Sequencing (NGS) has emerged as a key technology leading to revolutionary breakthroughs in numerous biomedical research areas. These technologies produce millions to billions of short DNA reads that represent a small fraction of the original target DNA sequence. These short reads contain little information individually but are produced at a high coverage of the original sequence such that many reads overlap. Overlap relationships allow for the reads to be linearly ordered and merged by computational programs called assemblers into long stretches of contiguous sequence called contigs that can be used for research applications. Although the assembly of the reads produced by NGS remains a difficult task, it is the process of extracting useful knowledge from these relatively short sequences that has become one of the most exciting and challenging problems in Bioinformatics. The assembly of short reads is an aggregative process where critical information is lost as reads are merged into contigs. In addition, the assembly process is treated as a black box, with generic assembler tools that do not adapt to input data set characteristics. Finally, as NGS data throughput continues to increase, there is an increasing need for smart parallel assembler implementations. In this dissertation, a new assembly approach called Focus is proposed. Unlike previous assemblers, Focus relies on a novel hybrid graph constructed from multiple graphs at different levels of granularity to represent the assembly problem, facilitating information capture and dynamic adjustment to input data set characteristics. This work is composed of four specific aims: 1) The implementation of a robust assembly and analysis tool built on the hybrid graph platform 2) The development and application of graph mining to extract biologically relevant features in NGS data sets 3) The integration of domain specific knowledge to improve the assembly and analysis process. 4) The construction of smart parallel computing approaches, including the application of energy-aware computing for NGS assembly and knowledge integration to improve algorithm performance. In conclusion, this dissertation presents a complete parallel assembler called Focus that is capable of extracting biologically relevant features directly from its hybrid assembly graph

Factor Fitting, Rank Allocation, and Partitioning in Multilevel Low Rank Matrices

We consider multilevel low rank (MLR) matrices, defined as a row and column permutation of a sum of matrices, each one a block diagonal refinement of the previous one, with all blocks low rank given in factored form. MLR matrices extend low rank matrices but share many of their properties, such as the total storage required and complexity of matrix-vector multiplication. We address three problems that arise in fitting a given matrix by an MLR matrix in the Frobenius norm. The first problem is factor fitting, where we adjust the factors of the MLR matrix. The second is rank allocation, where we choose the ranks of the blocks in each level, subject to the total rank having a given value, which preserves the total storage needed for the MLR matrix. The final problem is to choose the hierarchical partition of rows and columns, along with the ranks and factors. This paper is accompanied by an open source package that implements the proposed methods

Mullaorganismide biogeograafia

Väitekirja elektrooniline versioon ei sisalda publikatsiooneMullamikroobide ja -loomade rühmad reguleerivad maapealset elurikkust ja ökosüsteemide toimimist. Ülevaatelisi ja vaatlustel põhinevaid uuringuid tehes tuvastasin, kuidas ruumi, keskkonna ja taimeliikide muutused mõjutavad mullaorganismide kooslusi ja elurikkust ning millised ökoloogilised protsessid on peamiste organismirühmade koosluse varieeruvuse aluseks. Võtsin kasutusele taimede mükoriisa niširuumi (PMNS – plant mycorrhizal niche space) mõiste, mis tähistab taimede võimet kasutada ja kujundada mükoriissete seente kogumit. Selle väärtus sõltub taime mükoriissetest seostest ja funktsionaalsetest tunnustest. Lõin mudeli, et jaotada taimeliike erinevatesse PMNS-idesse, mis võimaldab ennustada mullas leiduvate mükoriissete seente kooslust konkreetses elupaigas. Lisaks määrasin taimeperekonna lepp (Alnus) liikide ja nendega seotud mükoriissete seente, ruumiliste, edaafiliste ja klimaatiliste tegurite suhtelise panuse mükoriissete juurtega seotud bakterikoosluste struktuuri. Leidsin, et mõned arvukad bakterite taksonid on liigispetsiifilised teatud lepaliikidele. Valikuprotsesside olulisus oli suurem väikesemate ja laiema nišiulatusega organismide kooslustes. Globaalse mullauuringu põhjal tuvastasin, et mulla pH ja aasta keskmine sademete hulk olid vastavalt eukarüootsete mikroobide ja loomade koosluste struktuuri peamised määrajad. Eukarüootide rühmadel esinesid vastandlikud elurikkuse mustrid laiuskraadi gradiendil. Minu doktoritöö viitab taimede funktsionaalsete tunnuste suurele tähtsusele mulla mükoriissete seenekoosluste struktureerimisel. Seened vahendavad taimedevahelist konkurentsi nii, sarnase PMNS-iga taimedel on negatiivne seos. Doktoritöö rõhutab ka biootiliste muutujate olulisust juurtega seotud bakterikoosluste kujundamisel ja näitab, et globaalses mastaabis on juurtega seotud ja mullabakterite koosluste aluseks erinevad bioloogilised protsessid. Mulla eukarüootidel esineb positiivne seos keha (raku) suuruse ja niši laiuse vahel ning nende biogeograafilisi mustreid juhtivate ökoloogiliste protsesside ja keskkonnategurite suhtelise mõju vahel.Belowground microbial and animal organism groups significantly regulate aboveground biodiversity and the functioning of terrestrial ecosystems. By conducting review and research studies, we examined how spatial, environmental, and plant species changes affect the belowground composition and diversity and what ecological processes underlie the community variations in association with organism functional groups. We introduced plant mycorrhizal niche space (PMNS) as a plant’s ability to exploit and shape the mycorrhizal fungal pool depending on its dependency on mycorrhizal status and plant functional traits. We provide a model to classify plant species into different PMNS, helping to predict soil mycorrhizal fungi community in a particular habitat by comparing PMNS distance between plant species. Further, we found that the Alnus species phylogeny was the primary determinant for the composition of root-associated bacterial communities, followed by edaphic, spatial and climate variables. In addition, we found Alnus species-specificity for some highly abundant bacterial phylotypes. Our analysis also showed that the importance of selection processes was higher in the community assemblage of smaller-bodied and wider niche breadth organisms. Soil pH and mean annual precipitation were the primary determinants of the community structure of eukaryotic microbes and animals, respectively. We further found contrasting latitudinal diversity patterns and strengths for soil eukaryotic microbes and animals. Taken together, this thesis shows the role of plant functional traits in structuring soil mycorrhizal communities mediating plant-to-plant competition such that there is a negative relation between the similarity of PMNS and the role of mycorrhizal fungi in plant invasion and alteration of mycorrhizal fungi following invasion. It also highlights the importance of biotic variables in shaping root-associated bacterial communities and shows that different processes underlie root-associated and soil bacterial communities on a global scale. Finally, our results point to a potential link between body size and niche breadth in soil eukaryotes and the relative effect of ecological processes and environmental factors in driving their biogeographic patterns.https://www.ester.ee/record=b550745

Kohalike ja invasiivsete röövtoiduliste suurselgrootute elupaigakasutus ja toitumissuhted Läänemere põhjaosas

Väitekirja elektrooniline versioon ei sisalda publikatsiooneRöövtoidulised suurselgrootud, peamiselt vähilaadsed, on rannikumere toitumisvõrgustikes oluliseks lüliks põhjaelustiku ja kalade vahel ning ühtlasi nad reguleerivad väiksemate selgrootute arvukust. Läänemere põhjaosas elas selle rühma esindajaid seni ainult kaks liiki – läänemere krevett (Palaemon adspersus) ja põhjamere garneel (Crangon crangon). Hiljuti lisandusid neile kohalikele liikidele kaks võõrliiki – elegantne krevett (Palaemon elegans) ja rändkrabi (Rhithropanopeus harrisii). Kohalike ja võõrliikidest röövtoiduliste suurselgrootute leviku, elupaigaeelistuste ja toitumise uurimiseks kasutati olemasolevaid põhjaelustiku leviku andmeid, spetsiaalselt uuritavatele liikidele suunatud proovide kogumist loodusest ja laborikatseid, kus rakendati muuhulgas loomade raadiomärgistamist. Võõrliigist kreveti levik oli ulatuslikum kui kohalike krevettide levik. Võõrliik oli kohalike krevettidega võrreldes enam seotud elupaikadega, millele on iseloomulikud etrofeerumise tunnused (kõrge toitainete kontsentratsioon, lühiealiste niitjate vetikate suur hulk). Krevettide toitumisuuringud näitasid, et uuritud Palaemon liikide toitumisintensiivsus ja toidu kooseis ei erinenud. Seega on kohaliku ja võõrkreveti roll rannikumere toiduvõrkudes sarnane, ent võõrliik võib troofilisi suhteid ümber kujundada piirkondades, kus kohalikud krevetid puuduvad. Kõige kitsama elupaigakasutusega oli põhjamere garneel ja Palaemon liikidest oli võõrliigi P. elegans spetsialiseerumise tase mõnevõrra kõrgem kui kohalikul liigil. R. harrisii eelistas põisadruga (Fucus vesiculosus) elupaika mis viitab sellele, et põisadruga elupaik pakub krabile aastaringset stabiilset elupaika ja et mitmekesine põhjakooslus võib saada seetõttu krabidest oluliselt mõjutatud. Doktoritöö tulemused näitasid, et elupaikade iseloom ja seisund mõjutab kohalike ja võõrliikide levikumustreid ning võõrliikidest selgrootute kiskjate saabumine ja kiire levila laienemine Läänemere põhjaosas toovad kaasa täiesti uue ökoloogilise funktsiooni (suuremõõtmeline kiskja) või juba varem regionaalselt esinenud funktsiooni leviku piirkondadesse, kus see varem puudus.Decapod crustaceans, such as crabs and shrimps play an important role in coastal ecosystems as they prey on small benthic invertebrates and at the same time they are an important food item for fishes. Until recently, this group of macroinvertebrates consisted of only a few species in the northern Baltic Sea, including only two species of native shrimps – Crangon crangon and Palaemon adspersus. However, very recently two non-native crustacean predators arrived – the shrimp Palaemon elegans and the crab Rhithropanopeus harrisii. Data from available databases were used together with field sampling and laboratory experiments (incl. radio frequency positioning technology) to describe the geographical distribution, habitat selection, and feeding of native and invasive predatory crustaceans in the coastal areas of the northern Baltic Sea. The distribution of the non-native P. elegans was wider than that of native species. P. elegans was associated with lower salinity, higher concentrations of nutrients and higher proportions of ephemeral filamentous algae, relative to P. adspersus. According to results of the experiment on feeding activity, P. elegans performs a similar role in the coastal food web as the native congener, although it may rearrange trophic interactions and introduce new ecological function in the most eutrophicated areas previously lacking any native shrimp. Among the studied shrimps, C. crangon had the highest habitat specialization. The non-native P. elegans showed slightly higher habitat specialization compared to the native P. adspersus. The invasive crab R. harrisii preferred habitats with bladder wrack where the diverse native community may become heavily impacted by this novel large-bodied predator. This thesis showed that the successful establishment of non-native predatory invertebrates can introduce new ecological functions (large-bodied predators) or considerably strengthen already existed ones, while the heterogeneity of habitats has varying effects on the distribution patterns of native and invasive species