With the ever-growing size of sequence data sets, data processing and analysis are an increasingly large portion of the time and money spent on nucleic acid sequencing projects. Correspondingly, the performance of the software and algorithms used to perform that analysis has a direct effect on the time and expense involved. Although the analytical methods are widely varied, certain types of software and algorithms are applicable to a number of areas. Targeting improvements to these common elements has the potential for wide reaching rewards. This dissertation research consisted of several projects to characterize and improve upon the efficiency of several common elements of sequence data analysis software and algorithms. The first project sought to improve the efficiency of the short read mapping process, as mapping is the most time consuming step in many data analysis pipelines. The result was a new short read mapping algorithm and software, demonstrated to be more computationally efficient than existing software and enabling more of the raw data to be utilized. While developing this software, it was discovered that a widely used bioinformatics software library introduced a great deal of inefficiency into the application. Given the potential impact of similar libraries to other applications, and because little research had been done to evaluate library efficiency, the second project evaluated the efficiency of seven of the most popular bioinformatics software libraries, written in C++, Java, Python, and Perl. This evaluation showed that two of libraries written in the most popular language, Java, were an order of magnitude slower and used more memory than expected based on the language in which they were implemented. The third and final project, therefore, was the development of a new general-purpose bioinformatics software library for Java. This library, known as BioMojo, incorporated a new design approach resulting in vastly improved efficiency. Assessing the performance of this new library using the benchmark methods developed for the second project showed that BioMojo outperformed all of the other libraries across all benchmark tasks, being up to 30 times more CPU efficient than existing Java libraries.

Thesis (Ph. D.)--Cornell University, January, 2009. / Vita. Includes bibliographical references (leaves 121-134).

Os vírus Influenza A infectam um largo espectro de hospedeiros e causam epidemias anuais. São vírus com alta variabilidade genética e RNA segmentado, que podem sofrer rearranjos entre os genes de diferentes vírus. Em 2006, foram analisadas 521 amostras de crianças menores de 5 anos atendidas no HU-USP e 25 foram positivas para Influenza A, sendo H3N2 o mais prevalente (68%). Cinco genes de 18 amostras foram seqüenciados e obtivemos 13 sequencias de HA, 12 da NP, 12 de NA, 14 da M e 10 da NS. Verificou-se a presença de várias mutações, especialmente na HA e NA, que favoreceram a substituição da cepa vacinal naquele ano. Todas as amostras H3N2 apresentaram sítios de resistências aos inibidores da M2. Diferentes linhagens circularam no mesmo ano, tanto de H1 como de H3, favorecendo rearranjos entre elas. Foram verificados, também rearranjos envolvendo os genes da HA e NP, indicando o complexo mecanismo de evolução desses vírus e enfatizando a necessidade de monitoramento da circulação e caracterização de seus genes. / Influenza A virus infects a wide range of hosts and cause annual outbreaks. RNA segmented virus has high genetic variability and may have rearrangements between the genes of different viruses. In 2006, 521 samples of children younger than 5 years were analyzed and 25 tested positive for Influenza A virus, of which the subtype H3N2 is the most prevalent (68%). Five genes of 18 samples were sequenced and 13 sequences of HA, 12 of NP, 14 of M and 10 of NS obtained were. The presence of this several mutations, especially in the HA and NA genes probably helped the replacement of the vaccine strain in that year. All H3N2 subtype samples showed points of resistance to M2 inhibitors. The phylogenetic analysis revealed the circulation of different lineages in the same year, for both H1 and H3, and the presence of two rearrangements involving the HA and NP genes. These results indicate the influence of rearrangements in the evolution of the virus and emphasize the need for monitoring of circulation and characterization of genes.

Os vírus Influenza A infectam um largo espectro de hospedeiros e causam epidemias anuais. São vírus com alta variabilidade genética e RNA segmentado, que podem sofrer rearranjos entre os genes de diferentes vírus. Em 2006, foram analisadas 521 amostras de crianças menores de 5 anos atendidas no HU-USP e 25 foram positivas para Influenza A, sendo H3N2 o mais prevalente (68%). Cinco genes de 18 amostras foram seqüenciados e obtivemos 13 sequencias de HA, 12 da NP, 12 de NA, 14 da M e 10 da NS. Verificou-se a presença de várias mutações, especialmente na HA e NA, que favoreceram a substituição da cepa vacinal naquele ano. Todas as amostras H3N2 apresentaram sítios de resistências aos inibidores da M2. Diferentes linhagens circularam no mesmo ano, tanto de H1 como de H3, favorecendo rearranjos entre elas. Foram verificados, também rearranjos envolvendo os genes da HA e NP, indicando o complexo mecanismo de evolução desses vírus e enfatizando a necessidade de monitoramento da circulação e caracterização de seus genes. / Influenza A virus infects a wide range of hosts and cause annual outbreaks. RNA segmented virus has high genetic variability and may have rearrangements between the genes of different viruses. In 2006, 521 samples of children younger than 5 years were analyzed and 25 tested positive for Influenza A virus, of which the subtype H3N2 is the most prevalent (68%). Five genes of 18 samples were sequenced and 13 sequences of HA, 12 of NP, 14 of M and 10 of NS obtained were. The presence of this several mutations, especially in the HA and NA genes probably helped the replacement of the vaccine strain in that year. All H3N2 subtype samples showed points of resistance to M2 inhibitors. The phylogenetic analysis revealed the circulation of different lineages in the same year, for both H1 and H3, and the presence of two rearrangements involving the HA and NP genes. These results indicate the influence of rearrangements in the evolution of the virus and emphasize the need for monitoring of circulation and characterization of genes.

O grupo de organoclorados, Bifenilas Policloradas (PCBs) é de difícil degradação e persistente no meio ambiente, tendo sido associado a diversos problemas nos organismos devido ao potencial toxicológico. Biodegradação constitui uma ferramenta eficaz e barata para remoção destes contaminantes do ambiente. O isolado RHA1 (fcb) de Rhodococcus sp. foi geneticamente construído com a introdução do operon de degradação hidrolítica de 4-clorobenzoato (fcb) para evitar a formação de produtos tóxicos durante a degradação de ácidos clorobenzóicos. Com o intuito de se obter informações sobre o processo adaptativo do recombinante Rhodococcus sp. isolado RHA1 (fcb) em substratos contendo PCBs, foram feitos dois ensaios avaliando-se a sobrevivência e o crescimento deste isolado. Rhodococcus sp. isolado RHA1 (fcb) foi inoculado (104 células.g-1) em substrato turfoso previamente irradiado a 50 KGy, contendo ou não 200 mg.Kg-1 de bifenilo. Em outro ensaio, além do recombinante, as bactérias Escherichia coli e Arthrobacter sp. foram inoculados em sedimento coletado na região do Estuário de Santos, contendo PHAs e PCBs, também irradiado (50 KGy). O crescimento das bactérias em ambos os substratos foi monitorado através de contagem de Unidades Formadoras de Colônias (UFCs). Algumas colônias eram selecionadas aleatoriamente para extração de DNA, detecção do operon fcb através de amplificação por PCR e sequenciamento do gene 16S rRNA. Aumento no número de UFCs nos tratamentos inoculados com o recombinante foi observado até 150 dias no ensaio com substrato turfoso e 70 dias na amostra ambiental. Entretanto, houve queda no número de UFCs após os 10 dias nos tratamentos inoculados com E. coli e Arthrobacter sp. Os genes fcbA e fcbB do operon fcb foram detectados nas colônias isoladas dos tratamentos inoculados com o isolado RHA1 (fcb) em ambos os substratos. A análise das seqüências pertencentes às colônias isoladas do tratamento inoculado com o isolado RHA1 (fcb) feita através de BLAST nos sites do NCBI e Ribossomal Database Project, apresentou 99% de identidade com a seqüência do gene ribossomal 16S de Rhodococcus sp. isolado ZC–3 (AM076672.1). Somente as seqüências referentes ao tratamento inoculado com E. coli foram analisadas, as quais apresentaram 99% de identidade com a seqüência do gene ribossomal 16S de E. coli isolado K-12 MG 1655 (U00096.2). Estes resultados sugerem que Rhodococcus sp. isolado RHA1 (fcb) cresce na turfa irradiada (até 150 dias) na presença e ausência de PCB e nesta amostra de sedimento irradiada (até 70 dias), com aparente estabilidade do operon fcb durante este período e nestas condições. A possível presença dos genes fcbB e fcbA em bactérias nativas crescidas em meio K1 com ácido 4- clorobenzóico isoladas do sedimento antes da irradiação, sugere a presença de bactérias do local com potencial biodegradador deste composto. / The group of organochlorates Biphenyl Polychlorates (PCBs) is of difficult degradation and persistent in the environment, being associated to several problems in the organisms due to its toxicological potential. The isolate RHA1 (fcb) from Rhodococcus sp. was genetically built with the introduction of the operon of hydrolytic degradation 4-chlorobenzoate (fcb) to avoid the formation of toxic products during the degradation of chlorobenzoic acids. In order to obtain information about the adaptative process of the recombinant Rhodococcus sp. isolate RHA1 (fcb) in substrates containing PCBs, two essays were made evaluating the survival and growth of this isolate. Rhodococcus sp. isolate RHA1 (fcb) was inoculated (104 cells.g-1) in peat substrate previously irradiated with 50 kGy, with and without 200 mg.kg-1 of biphenyl. In another essay, besides of the recombinant, the bacteria Escherichia coli and Arthrobacter sp. were inoculated in soil, also irradiated (50 kGy), from the Estuário de Santos region containing PHAs and PCBs. The growth of the bacteria in both substrates was monitorated counting the Colony Forming Units (CFUs). Some colonies were selected randomly for DNA extraction, fcb operon detection through PCR, and sequencing of the 16S rRNA gene. Rising in the number of CFUs in the recombinant inoculated treatments was observed until 150 days in the essay with peat substrate, and until 70 days in the environmental sample. Nonetheless, there was a reduction in the number of CFUs after 10 days in the treatment inoculated with E. coli and Arthrobacter sp. The genes fcbA and fcbB from the operon fcb were detected in the isolated colonies of the treatments inoculated with the isolate RHA1 (fcb) in both substrates. The analysis of the sequences belonging to the colonies isolated from the treatment inoculated with the isolate RHA1 (fcb) through BLAST in the NCBI and Ribosomal Database Project sites showed 99% identity with the sequence of the gene 16S ribosomal from Rhodococcus sp. isolate ZC-3 (AM076672.1). Only the sequences referring to the treatment inoculated with E. coli were analyzed, which showed 99% identity with the sequence of the 16S ribosomal gene from E. coli isolate K-12 MG 1655 (U00096.2). These results suggest that Rhodococcus sp. isolate RHA1 (fcb) grows in the peat irradiated (until 150 days), in the presence and absence of PCB and in this irradiated sediment sample (until 70 days), with apparent stability of the fcb operon during this period and in these conditions. The possible presence of the fcbA and fcbB genes in native bacteria grown in K1 medium with 4-chlorobenzoate acid isolated from sediment before irradiation suggests the presence of native bacteria with biodegradation potential of this compound.

The research object is probabilistic properties of non-coding DNA (nucleotide) sequences. Available models of DNA sequences are reviewed and their basic assumptions are verified by statistical analysis of bacterial DNA sequences. On the ground of this analysis, the definition of non-informative genetic sequence is introduced and a mathematical model of “genetic noise” is proposed. Computer simulations of non-coding (non-informative) nucleotide sequence evolution are performed and resulting sequences are compared with native ones. The task of visualisation of genetic sequences is an important part of the work. The main tasks of the work are the following: 1. to analyse the statistical features (independence, Markovity, long-range dependence, etc.) of bacterial DNA sequences, especially non-coding ones, 2. to formulate a definition of a non-informative nucleotide sequence (“genetic noise”) and to propose its mathematical model, 3. using the methodology of functional data analysis and the distance metrics between oligonucleotides, to propose an efficient method for nucleotide sequence visualisation. General Conclusions: 1. The probability model of non-informative nucleotide sequence or, in other words, “genetic noise” (an analogue of the “white noise”) is proposed and its properties are studied mainly by computer simulation. The long-range dependence in DNA sequences has been extensively studied and is considered as an evidence of their complexity and hierarchical structure... [to full text]

The research object is probabilistic properties of non-coding DNA (nucleotide) sequences. Available models of DNA sequences are reviewed and their basic assumptions are verified by statistical analysis of bacterial DNA sequences. On the ground of this analysis, the definition of non-informative genetic sequence is introduced and a mathematical model of “genetic noise” is proposed. Computer simulations of non-coding (non-informative) nucleotide sequence evolution are performed and resulting sequences are compared with native ones. The task of visualisation of genetic sequences is an important part of the work. The main tasks of the work are the following: 1. to analyse the statistical features (independence, Markovity, long-range dependence, etc.) of bacterial DNA sequences, especially non-coding ones, 2. to formulate a definition of a non-informative nucleotide sequence (“genetic noise”) and to propose its mathematical model, 3. using the methodology of functional data analysis and the distance metrics between oligonucleotides, to propose an efficient method for nucleotide sequence visualisation. General Conclusions: 1. The probability model of non-informative nucleotide sequence or, in other words, “genetic noise” (an analogue of the “white noise”) is proposed and its properties are studied mainly by computer simulation. The long-range dependence in DNA sequences has been extensively studied and is considered as an evidence of their complexity and hierarchical structure... [to full text]

O grupo de organoclorados, Bifenilas Policloradas (PCBs) é de difícil degradação e persistente no meio ambiente, tendo sido associado a diversos problemas nos organismos devido ao potencial toxicológico. Biodegradação constitui uma ferramenta eficaz e barata para remoção destes contaminantes do ambiente. O isolado RHA1 (fcb) de Rhodococcus sp. foi geneticamente construído com a introdução do operon de degradação hidrolítica de 4-clorobenzoato (fcb) para evitar a formação de produtos tóxicos durante a degradação de ácidos clorobenzóicos. Com o intuito de se obter informações sobre o processo adaptativo do recombinante Rhodococcus sp. isolado RHA1 (fcb) em substratos contendo PCBs, foram feitos dois ensaios avaliando-se a sobrevivência e o crescimento deste isolado. Rhodococcus sp. isolado RHA1 (fcb) foi inoculado (104 células.g-1) em substrato turfoso previamente irradiado a 50 KGy, contendo ou não 200 mg.Kg-1 de bifenilo. Em outro ensaio, além do recombinante, as bactérias Escherichia coli e Arthrobacter sp. foram inoculados em sedimento coletado na região do Estuário de Santos, contendo PHAs e PCBs, também irradiado (50 KGy). O crescimento das bactérias em ambos os substratos foi monitorado através de contagem de Unidades Formadoras de Colônias (UFCs). Algumas colônias eram selecionadas aleatoriamente para extração de DNA, detecção do operon fcb através de amplificação por PCR e sequenciamento do gene 16S rRNA. Aumento no número de UFCs nos tratamentos inoculados com o recombinante foi observado até 150 dias no ensaio com substrato turfoso e 70 dias na amostra ambiental. Entretanto, houve queda no número de UFCs após os 10 dias nos tratamentos inoculados com E. coli e Arthrobacter sp. Os genes fcbA e fcbB do operon fcb foram detectados nas colônias isoladas dos tratamentos inoculados com o isolado RHA1 (fcb) em ambos os substratos. A análise das seqüências pertencentes às colônias isoladas do tratamento inoculado com o isolado RHA1 (fcb) feita através de BLAST nos sites do NCBI e Ribossomal Database Project, apresentou 99% de identidade com a seqüência do gene ribossomal 16S de Rhodococcus sp. isolado ZC–3 (AM076672.1). Somente as seqüências referentes ao tratamento inoculado com E. coli foram analisadas, as quais apresentaram 99% de identidade com a seqüência do gene ribossomal 16S de E. coli isolado K-12 MG 1655 (U00096.2). Estes resultados sugerem que Rhodococcus sp. isolado RHA1 (fcb) cresce na turfa irradiada (até 150 dias) na presença e ausência de PCB e nesta amostra de sedimento irradiada (até 70 dias), com aparente estabilidade do operon fcb durante este período e nestas condições. A possível presença dos genes fcbB e fcbA em bactérias nativas crescidas em meio K1 com ácido 4- clorobenzóico isoladas do sedimento antes da irradiação, sugere a presença de bactérias do local com potencial biodegradador deste composto. / The group of organochlorates Biphenyl Polychlorates (PCBs) is of difficult degradation and persistent in the environment, being associated to several problems in the organisms due to its toxicological potential. The isolate RHA1 (fcb) from Rhodococcus sp. was genetically built with the introduction of the operon of hydrolytic degradation 4-chlorobenzoate (fcb) to avoid the formation of toxic products during the degradation of chlorobenzoic acids. In order to obtain information about the adaptative process of the recombinant Rhodococcus sp. isolate RHA1 (fcb) in substrates containing PCBs, two essays were made evaluating the survival and growth of this isolate. Rhodococcus sp. isolate RHA1 (fcb) was inoculated (104 cells.g-1) in peat substrate previously irradiated with 50 kGy, with and without 200 mg.kg-1 of biphenyl. In another essay, besides of the recombinant, the bacteria Escherichia coli and Arthrobacter sp. were inoculated in soil, also irradiated (50 kGy), from the Estuário de Santos region containing PHAs and PCBs. The growth of the bacteria in both substrates was monitorated counting the Colony Forming Units (CFUs). Some colonies were selected randomly for DNA extraction, fcb operon detection through PCR, and sequencing of the 16S rRNA gene. Rising in the number of CFUs in the recombinant inoculated treatments was observed until 150 days in the essay with peat substrate, and until 70 days in the environmental sample. Nonetheless, there was a reduction in the number of CFUs after 10 days in the treatment inoculated with E. coli and Arthrobacter sp. The genes fcbA and fcbB from the operon fcb were detected in the isolated colonies of the treatments inoculated with the isolate RHA1 (fcb) in both substrates. The analysis of the sequences belonging to the colonies isolated from the treatment inoculated with the isolate RHA1 (fcb) through BLAST in the NCBI and Ribosomal Database Project sites showed 99% identity with the sequence of the gene 16S ribosomal from Rhodococcus sp. isolate ZC-3 (AM076672.1). Only the sequences referring to the treatment inoculated with E. coli were analyzed, which showed 99% identity with the sequence of the 16S ribosomal gene from E. coli isolate K-12 MG 1655 (U00096.2). These results suggest that Rhodococcus sp. isolate RHA1 (fcb) grows in the peat irradiated (until 150 days), in the presence and absence of PCB and in this irradiated sediment sample (until 70 days), with apparent stability of the fcb operon during this period and in these conditions. The possible presence of the fcbA and fcbB genes in native bacteria grown in K1 medium with 4-chlorobenzoate acid isolated from sediment before irradiation suggests the presence of native bacteria with biodegradation potential of this compound.