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    Wyświetlanie 1-11 z 11
    Tytuł:
    Some remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmark
    Autorzy:
    Błażewicz, J.
    Formanowicz, P.
    Wojciechowski, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/930013.pdf
    Data publikacji:
    2009
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    dostosowanie odniesienia
    dokładność ustawienia
    multiple sequence alignment
    reference alignment
    alignment accuracy
    Opis:
    BAliBASE is one of the most widely used benchmarks for multiple sequence alignment programs. The accuracy of alignment methods is measured by bali score-an application provided together with the database. The standard accuracy measures are the Sum of Pairs (SP) and the Total Column (TC). We have found that, for non-core block columns, results calculated by bali score are different from those obtained on the basis of the formal definitions of the measures. We do not claim that one of these measures is better than the other, but they are definitely different. Such a situation can be the source of confusion when alignments obtained using various methods are compared. Therefore, we propose a new nomenclature for the measures of the quality of multiple sequence alignments to distinguish which one was actually calculated. Moreover, we have found that the occurrence of a gap in some column in the first sequence of the reference alignment causes column discarding.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2009, 19, 4; 675-678
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Motifs of the caldesmon family.
    Autorzy:
    Czuryło, Edward
    Powiązania:
    https://bibliotekanauki.pl/articles/1044222.pdf
    Data publikacji:
    2000
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    secondary structure prediction
    caldesmon
    binding sites
    conserved sequences
    multiple sequence alignment
    Opis:
    Seven highly conserved regions were found in caldesmon molecules from various sources using the multiple sequence alignment method. Their localization coincides with regions where the binding sites to other proteins were postulated. Less conserved and highly divergent regions of the sequences are described as well. These results could refine the planning of caldesmon gene manipulations and accelerate the precise localization of binding sites in the caldesmon molecule and, as a consequence, this could help to elucidate its function in smooth muscle contraction.
    Źródło:
    Acta Biochimica Polonica; 2000, 47, 4; 1019-1026
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    G-DNA – a highly efficient multi-GPU/MPI tool for aligning nucleotide reads
    Autorzy:
    Frohmberg, W.
    Kierzynka, M.
    Blazewicz, J.
    Gawron, P.
    Wojciechowski, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/200827.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    DNA assembly preprocessing
    sequence alignment
    GPU computing
    Opis:
    DNA/RNA sequencing has recently become a primary way researchers generate biological data for further analysis. Assembling algorithms are an integral part of this process. However, some of them require pairwise alignment to be applied to a great deal of reads. Although several efficient alignment tools have been released over the past few years, including those taking advantage of GPUs (Graphics Processing Units), none of them directly targets high-throughput sequencing data. As a result, a need arose to create software that could handle such data as effectively as possible. G-DNA (GPU-based DNA aligner) is the first highly parallel solution that has been optimized to process nucleotide reads (DNA/RNA) from modern sequencing machines. Results show that the software reaches up to 89 GCUPS (Giga Cell Updates Per Second) on a single GPU and as a result it is the fastest tool in its class. Moreover, it scales up well on multiple GPUs systems, including MPI-based computational clusters, where its performance is counted in TCUPS (Tera CUPS).
    Źródło:
    Bulletin of the Polish Academy of Sciences. Technical Sciences; 2013, 61, 4; 989-992
    0239-7528
    Pojawia się w:
    Bulletin of the Polish Academy of Sciences. Technical Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    MIPS sequences: a promising molecular consideration in angiosperm phylogeny and systematics
    Autorzy:
    Hazra, A.
    Nandy, P.
    Sengupta, C.
    Das, S.
    Powiązania:
    https://bibliotekanauki.pl/articles/80785.pdf
    Data publikacji:
    2018
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    myo-inositol-1-phosphate synthase
    protein sequence
    angiosperm
    phylogenesis
    maximum likelihood method
    multiple sequence alignment
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2018, 99, 1
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    An example of template based protein structure modeling by global optimization
    Autorzy:
    Joo, K.
    Joung, I.
    Lee, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/1938628.pdf
    Data publikacji:
    2016
    Wydawca:
    Politechnika Gdańska
    Tematy:
    template based modeling
    protein structure modeling
    global optimization
    casp
    homology modeling
    sequence alignment
    fold recognition
    Opis:
    CASP (Critical Assessment of protein Structure Prediction) is a community-wide experiment for protein structure prediction taking place every two years since 1994. In CASP 11 held in 2014, according to the official CASP 11 assessment, our method named `nns' was ranked as the second best server method based on models ranked as first out of 81 targets. In `nns', we applied the powerful global optimization method of conformational space annealing to three stages of optimization, including multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain remodeling. For the fold recognition, a new alignment method called CRF align was used. The good performance of the nns server method is attributed to the successful fold recognition carried out by combined methods including CRF align, and the current modeling formulation incorporating accurate structural aspects collected from multiple templates. In this article, we provide a successful example of `nns' predictions for T0776, for which all details of intermediate modeling data are provided.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 341-352
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Application of bioinformatics methods to recognition of network threats
    Autorzy:
    Kozakiewicz, A.
    Felkner, A.
    Kijowski, P.
    Kruk, T. J.
    Powiązania:
    https://bibliotekanauki.pl/articles/308561.pdf
    Data publikacji:
    2007
    Wydawca:
    Instytut Łączności - Państwowy Instytut Badawczy
    Tematy:
    network threat analysis
    sequence alignment
    edit distance
    bioinformatics
    Opis:
    Bioinformatics is a large group of methods used in biology, mostly for analysis of gene sequences. The algorithms developed for this task have recently found a new application in network threat detection. This paper is an introduction to this area of research, presenting a survey of bioinformatics methods applied to this task, outlining the individual tasks and methods used to solve them. It is argued that the early conclusion that such methods are ineffective against polymorphic attacks is in fact too pessimistic.
    Źródło:
    Journal of Telecommunications and Information Technology; 2007, 4; 23-27
    1509-4553
    1899-8852
    Pojawia się w:
    Journal of Telecommunications and Information Technology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Correlated mutations in selected protein families
    Autorzy:
    Leluk, J.
    Sobczyk, M.
    Becella, Ł.
    Powiązania:
    https://bibliotekanauki.pl/articles/1986920.pdf
    Data publikacji:
    2002
    Wydawca:
    Politechnika Gdańska
    Tematy:
    protein sequence
    multiple alignment
    tertiary structure
    mutational correlation
    genetic semihomology algorithm
    Opis:
    Four different protein families (two proteinase inhibitor families, myoglobins and lysozymes) were surveyed for correlated mutations with respect to the position distance and their significance in structure stabilization and biological activity. They were chosen for this study in order to verify the currently admitted model of mutational correlation relationship with respect to spatial contact of the residues and contribution in protein biological activity. There was observed high contribution of spatially dispersed residues (which are also not involved in the protein active center) in mutational correlation. Because of the significantly large distance between correlated positions these cases do not correspond explicitly to any mechanism included in current hypotheses. It is suggested that the role of residue spatial contact in structure preservation, intermolecular interaction and active site rescue mechanisms only partially explains the correlation phenomenon.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2002, 6, 3; 469-482
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Application of genetic semihomology algorithm to theoretical studies on various protein families.
    Autorzy:
    Leluk, Jacek
    Hanus-Lorenz, Beata
    Sikorski, Aleksander
    Powiązania:
    https://bibliotekanauki.pl/articles/1044159.pdf
    Data publikacji:
    2001
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    multiple alignment
    cryptic mutations
    genetic semihomology
    sequence consensus
    Opis:
    Several protein families of different nature were studied for genetic relationship, correct alignment at non-homologous fragments, optimal sequence consensus construction, and confirmation of their actual relevance. A comparison of the genetic semihomology approach with statistical approaches indicates a high accuracy and cognition significance of the former. This is particularly pronounced in the study of related proteins that show a low degree of homology. The sequence multiple alignments were verified and corrected with respect to the questionable, non-homologous fragments. The verified alignments were the basis for consensus sequence formation. The frequency of six-codon amino acids occurrence versus position variability was studied and their possible role in amino acid mutational exchange at variable positions is discussed.
    Źródło:
    Acta Biochimica Polonica; 2001, 48, 1; 21-33
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    A novel tetrameric lectin from Lycoris aurea with four mannose binding sites per monomer
    Autorzy:
    Liu, Jiwei
    Xu, Xiaochao
    Liu, Jinzhi
    Balzarini, Jan
    Luo, Yongtin
    Kong, Yang
    Li, Jian
    Chen, Fang
    Van Damme, Els
    Bao, Jinku
    Powiązania:
    https://bibliotekanauki.pl/articles/1041131.pdf
    Data publikacji:
    2007
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    sequence alignment
    mannose-binding lectin
    Lycoris aurea agglutinin
    molecular modeling and docking
    Opis:
    The mannose-binding agglutinin from bulbs of Lycoris aurea (LAA) agglutinates rabbit but not human erythrocytes. The molecular mass of the monomer in SDS/PAGE is 12 kDa while the apparent molecular mass in gel filtration is 48 kDa, indicating that LAA is a homotetramer. The full-length cDNA of LAA contains 683 bp with an open reading frame encoding a protomer of 162 amino-acid residues. Hydrophobic Cluster Analysis and molecular modeling of the 109-residue mature polypeptide suggested a similar secondary and tertiary structure to those of Narcissus pseudonarcissus agglutinin (NPA). Molecular docking revealed that, besides the three mannose-binding sites common among Amaryllidaceae lectins, LAA also contains a fourth unique mannose-binding site formed by a tryptophan cluster. The existence of four mannose-binding sites in each monomer of LAA is very unusual and has only been reported for NPA earlier.
    Źródło:
    Acta Biochimica Polonica; 2007, 54, 1; 159-166
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    A novel approach for identifying DNA repair pathways proteins using an evolutionary approach: Plasmodium falciparum case study
    Autorzy:
    Milanowska, K.
    Wojtczak, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/80413.pdf
    Data publikacji:
    2016
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    DNA repair
    pathway
    ortholog
    pipeline
    Plasmodium falciparum
    proteomics
    protein
    profile analysis
    Hidden Markov model
    multiple sequence alignment
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2016, 97, 4
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Efficient alternatives to PSI-BLAST
    Autorzy:
    Startek, M.
    Lasota, S.
    Sykulski, M.
    Bułak, A.
    Noé, L.
    Kucherov, G.
    Gambin, A.
    Powiązania:
    https://bibliotekanauki.pl/articles/201603.pdf
    Data publikacji:
    2012
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    PSI BLAST tool
    sequence alignment
    seeding technique
    Opis:
    In this paper we present two algorithms that may serve as efficient alternatives to the well-known PSI BLAST tool: SeedBLAST and CTX-PSI Blast. Both may benefit from the knowledge about amino acid composition specific to a given protein family: SeedBLAST uses the advisedly designed seed, while CTX-PSI BLAST extends PSI BLAST with the context-specific substitution model. The seeding technique became central in the theory of sequence alignment. There are several efficient tools applying seeds to DNA homology search, but not to protein homology search. In this paper we fill this gap. We advocate the use of multiple subset seeds derived from a hierarchical tree of amino acid residues. Our method computes, by an evolutionary algorithm, seeds that are specifically designed for a given protein family. The seeds are represented by deterministic finite automata (DFAs) and built into the NCBI-BLAST software. This extended tool, named SeedBLAST, is compared to the original BLAST and PSI-BLAST on several protein families. Our results demonstrate a superiority of SeedBLAST in terms of efficiency, especially in the case of twilight zone hits. The contextual substitution model has been proven to increase sensitivity of protein alignment. In this paper we perform a next step in the contextual alignment program. We announce a contextual version of the PSI-BLAST algorithm, an iterative version of the NCBI-BLAST tool. The experimental evaluation has been performed demonstrating a significantly higher sensitivity compared to the ordinary PSI-BLAST algorithm.
    Źródło:
    Bulletin of the Polish Academy of Sciences. Technical Sciences; 2012, 60, 3; 495-505
    0239-7528
    Pojawia się w:
    Bulletin of the Polish Academy of Sciences. Technical Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-11 z 11

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