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Relevant bibliographies by topics / Homology search / Dissertations / Theses

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Dissertations / Theses on the topic 'Homology search'

Author: Grafiati

Published: 4 June 2021

Last updated: 19 February 2022

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1

Syed, Intikhab Alam Syed Intikhab Alam Syed Intikhab Alam. "Integrative approaches to protein homology search." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=975814540.

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2

Alam, Intikhab. "Integrative approaches to protein homology search." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=975814540.

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3

Cameron, Michael, and mcam@mc-mc net. "Efficient Homology Search for Genomic Sequence Databases." RMIT University. Computer Science and Information Technology, 2006. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20070509.162443.

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Genomic search tools can provide valuable insights into the chemical structure, evolutionary origin and biochemical function of genetic material. A homology search algorithm compares a protein or nucleotide query sequence to each entry in a large sequence database and reports alignments with highly similar sequences. The exponential growth of public data banks such as GenBank has necessitated the development of fast, heuristic approaches to homology search. The versatile and popular blast algorithm, developed by researchers at the US National Center for Biotechnology Information (N

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4

Cooper, Gina Marie. "IMPROVING REMOTE HOMOLOGY DETECTION USING A SEQUENCE PROPERTY APPROACH." Wright State University / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=wright1251308636.

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5

Renkawitz, Jörg. "Monitoring homology search during DNA double-strand break repair in vivo." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-169454.

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6

Anstett, Benjamin [Verfasser], and Peter [Akademischer Betreuer] Becker. "Homology search guidance by the yeast recombination enhancer / Benjamin Anstett ; Betreuer: Peter Becker." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2017. http://d-nb.info/1132995329/34.

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7

Lee, Tsung-Lu. "BAXQLB̲LAST an enhanced BLAST bioinformatics homology search tool with batch and structured query support /." [Gainesville, Fla.] : University of Florida, 2002. http://purl.fcla.edu/fcla/etd/UFE1001161.

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8

Renkawitz, Jörg [Verfasser], and Stefan [Akademischer Betreuer] Jentsch. "Monitoring homology search during DNA double-strand break repair in vivo / Jörg Renkawitz. Betreuer: Stefan Jentsch." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2013. http://d-nb.info/1050648188/34.

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9

Freyhult, Eva. "A Study in RNA Bioinformatics : Identification, Prediction and Analysis." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8305.

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10

Gajdoš, Pavel. "Vyhledávání homologních enzymů." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2016. http://www.nusl.cz/ntk/nusl-255409.

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Tato práce se zabývá vyhledáváním homologních enzymů v proteinových databázích, jejímž cílem je navrhnout nástroj poskytující takové vyhledávání. Čtenář se seznámí se základní teorií týkající se proteinů, enzymů, homologie, ale také s existujícími nástroji pro vyhledávání homologních proteinů a enzymů. Dále je popsáno ohodnocení nalezených existujících nástrojů pro vyhledávání homologních enzymů. Pro potřeby vyhodnocení byla vytvořena datová sada spolu s algoritmem pro vyhodnocení vyýsledků jednotlivých nástrojů. Další částí práce je návrh a implementace nové metody pro vyhledávání homologních

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11

Darbha, Sriram. "RNA Homology Searches Using Pair Seeding." Thesis, University of Waterloo, 2005. http://hdl.handle.net/10012/1172.

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Due to increasing numbers of non-coding RNA (ncRNA) being discovered recently, there is interest in identifying homologs of a given structured RNA sequence. Exhaustive homology searching for structured RNA molecules using covariance models is infeasible on genome-length sequences. Hence, heuristic methods are employed, but they largely ignore structural information in the query. We present a novel method, which uses secondary structure information, to perform homology searches for a structured RNA molecule. We define the concept of a <em>pair seed</em> and theoretically model alignment

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12

Bussotti, Giovanni 1983. "Detecting and comparing non-coding RNAs." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/128970.

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In recent years there has been a growing interest in the field of non-coding RNA. This surge is a direct consequence of the discovery of a huge number of new non-coding genes, and of the finding that many of these transcripts are involved in key cellular functions. In this context, accurately detecting and comparing RNA sequences becomes extremely important. Aligning nucleotide sequences is one of the main requisite when searching for homologous genes. Accurate alignments reveal evolutionary relationships, conserved regions and more generally, any biologically relevant pattern. Comparing RNA m

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13

Bundschuh, Julia. "Molecular studies in gorgonian alloimmunity : search for gene homologs of the immunoglobulin gene superfamily in Swiftia exserta." FIU Digital Commons, 1991. http://digitalcommons.fiu.edu/etd/1942.

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Humoral and cells surface molecules of the mammalian immune system, grouped into the Immunoglobulin Gene Superfamily, share protein structure and gene sequence homologies with molecules found among diverse phylogenetic groups. In histocompatibility studies, the gorgonian coral Swiftia exserta has recently demonstrated specific alloimmunity with memory (Salter-Cid and Bigger, 1991. Biological Bulletin Vol 181). In an attempt to shed light on the origins of this gene family and the evolution of the vertebrate immune response, genomic DNA from Swiftia exserta was isolated, purified, and analyzed

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14

Nichio, Bruno Thiago de Lima. "Consolidação e validação da ferramenta Rapid Alignment Free Tool for Sequences Similarity Search to Groups (RAFTS3GROUPS) : um software rápido de clusterização para big data e buscador consistente de proteínas ortólogas." reponame:Repositório Institucional da UFPR, 2016. http://hdl.handle.net/1884/49076.

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Orientador : Prof. Dr. Roberto Tadeu Raittz<br>Coorientadores : Dra. Jeroniza Nunes Marchaukoski e Dr. Vinícius Almir Weiss<br>Dissertação (mestrado) - Universidade Federal do Paraná, Setor de Educação Profissional e Tecnológica, Programa de Pós-Graduação em Bioinformática. Defesa: Curitiba, 16/09/2016<br>Inclui referências ao final dos capítulos<br>Resumo: Uma das principais análises envolvendo sequências biológicas, imprescindíveis e complexas, é a análise de homologia. A necessidade de desenvolver técnicas e ferramentas computacionais que consigam predizer com mais eficiência grupos de ortó

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15

Yazbeck, Ali. "Improved Workflows for RNA Homology Search." 2019. https://ul.qucosa.de/id/qucosa%3A34681.

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Non-coding RNAs are the most abundant class of RNAs found throughout genomes. These RNAs are key players of gene regulation and thus, the func- tion of whole organisms. Numerous methods have been developed so far for detecting novel classes of ncRNAs or finding homologs to the known ones. Because of their abundance, the sequence availability of these RNAs is rapidly increasing, as is the case for example for microRNAs. However, for classes of them, still only incomplete information is available, invertebrates 7SK snRNA for instance. Consequently, a lot of false positive outputs are produced in

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16

Alam, Intikhab [Verfasser]. "Integrative approaches to protein homology search / by Intikhab Alam." 2005. http://d-nb.info/975814540/34.

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17

Yuen, Denis. "SPIDER: Reconstructive Protein Homology Search with De Novo Sequencing Tags." Thesis, 2011. http://hdl.handle.net/10012/5853.

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In the field of proteomic mass spectrometry, proteins can be sequenced by two independent yet complementary algorithms: de novo sequencing which uses no prior knowledge and database search which relies upon existing protein databases. In the case where an organism’s protein database is not available, the software Spider was developed in order to search sequence tags produced by de novo sequencing against a database from a related organism while accounting for both errors in the sequence tags and mutations. This thesis further develops Spider by using the concept of reconstruction in order to

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18

Gruber, Andreas R., Carsten Kilgus, Axel Mosig, Ivo L. Hofacker, Wolfgang Hennig, and Peter F. Stadler. "Arthropod 7SK RNA." 2008. https://ul.qucosa.de/id/qucosa%3A32793.

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The 7SK small nuclear RNA (snRNA) is a key player in the regulation of polymerase (pol) II transcription. The 7SK RNA was long believed to be specific to vertebrates where it is highly conserved. Homologs in basal deuterostomes and a few lophotrochozoan species were only recently reported. On longer timescales, 7SK evolves rapidly with only few conserved sequence and structure motifs. Previous attempts to identify the Drosophila homolog thus have remained unsuccessful despite considerable efforts. Here we report on the discovery of arthropod 7SK RNAs using a novel search strategy based on pol

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19

Hertel, Jana, Jong Danielle de, Manja Marz, Dominic Rose, Hakim Tafer, Andrea Tanzer, Bernd Schierwater, and Peter F. Stadler. "Non-coding RNA annotation of the genome of Trichoplax adhaerens." 2009. https://ul.qucosa.de/id/qucosa%3A32946.

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A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs—in particular rRNAs, tRNAs and some snRNAs—we developed a semi-global dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRN

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