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81.
Vinga S Carvalho AM Francisco AP Russo LM Almeida JS 《Algorithms for molecular biology : AMB》2012,7(1):10-12
Background
Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2 -L distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations.Results
The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm.Conclusions
The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems. 相似文献82.
Sohrab?P?Shah Yong?Huang Tao?Xu Macaire?MS?Yuen John?Ling BF?Francis?OuelletteEmail author 《BMC bioinformatics》2005,6(1):34
Background
We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. 相似文献83.
84.
OI Klychnikov AV Drabkin OV Vasilenko YS Pavlov MS Trofimova IN Smolenskaya AA Rozenkranz AS Sobolev AV Babakov 《Biochemistry. Biokhimii?a》1998,63(9):1083-1089
Higher plant plasma membranes carry receptors of different affinity for the phytotoxin fusicoccin. Reception of fusicoccin involves proteins belonging to the highly conserved 14-3-3 family, but the complete structure of the fusicoccin receptor (FCR) is unknown. Using radiation inactivation analysis, we estimated the molecular masses of low-affinity and high-affinity FCR at 63 +/- 7 and 130 +/- 15 kD, respectively. The dose dependences of receptor inactivation indicate that microsomal specimens contain "silent" FCRs of 420 +/- 90 kD in amounts commensurate with that of the active FCRs. Both low- and high-affinity FCRs are inactivated by hydrolytic enzymes from the outer surface of the plasma membrane, and impairment of protoplast integrity causes an irreversible transition of the low-affinity binding site into the high-affinity one. A scheme is proposed for the organization of different types of FCR in the plasma membrane, implying that the membrane affinity for fusicoccin reflects the interaction between proteins in the FCR complex. 相似文献
85.
Biotinyl-oligosaccharides are a relatively new generation of saccharide
probes that enable immobilization of desired oligosaccharides on
streptavidin matrices for studies of carbohydrate-protein interactions.
Here we describe the facile preparation of biotinyl-l-3-(2-naphthyl)-
alanine hydrazide (BNAH) derivatives of oligosaccharides, containing a
strong UV absorbing and fluorescent group, in which the ring of the
reducing-end monosaccharide is nonreduced. We evaluate reactivities of
immobilized BNAH- N -glycans with plant lectins that recognize aspects of
the oligosaccharide core or outer-arms. We make some comparisons with
2-amino-6-amidobiotinyl-pyridine (BAP) derivatives obtained by reductive
amination, and 6-(biotinyl)-aminocaproyl-hydrazide (BACH) derivatives which
have a longer spacer-arm. N -Glycan-BNAH and-BAP derivatives have, overall,
comparable reactivities with lectins which recognize N -glycan outer-arms
or the trimannosyl core, but only BNAH and BACH derivatives are bound by
lectins which recognize the non- reduced core. Moreover, with Pisum sativum
agglutinin (PSA) which additionally requires the fucosyl- N-
glycan-asparaginyl core for high affinity binding, the immobilized BNAH
derivative (which is an alanine hydrazide beta-glycoside) can substitute
for the natural beta- glycosylasparaginyl core, whereas the BACH derivative
(aminocaproyl- hydrazide-beta-glycoside) is less effective. BNAH is a
derivatization reagent of choice, therefore, for solid phase
carbohydrate-binding experiments with immobilized N -glycans.
相似文献
86.
The core domain of retrotransposon integrase in Hordeum: predicted structure and evolution 总被引:1,自引:0,他引:1
Suoniemi A; Tanskanen J; Pentikainen O; Johnson MS; Schulman AH 《Molecular biology and evolution》1998,15(9):1135-1144
Propagation of long terminal repeat (LTR)-bearing retrotransposons and
retroviruses requires integrase (IN, EC 2.7.7.-), encoded by the
retroelements themselves, which mediates the insertion of cDNA copies back
into the genome. An active retrotransposon family, BARE-1, comprises
approximately 7% of the barley (Hordeum vulgare subsp. vulgare) genome. We
have generated models for the secondary and tertiary structure of BARE-1 IN
and demonstrate their similarity to structures for human immunodeficiency
virus 1 and avian sarcoma virus INs. The IN core domains were compared for
80 clones from 28 Hordeum accessions representative of the diversity of the
genus. Based on the structural model, variations in the predicted, aligned
translations from these clones would have minimal structural and functional
effects on the encoded enzymes. This indicates that Hordeum retrotransposon
IN has been under purifying selection to maintain a structure typical of
retroviral INs. These represent the first such analyses for plant INs.
相似文献
87.
Rossi MS; Barrio E; Latorre A; Quezada-Diaz JE; Hasson E; Moya A; Fontdevila A 《Molecular biology and evolution》1996,13(2):314-323
Both original and colonizer populations of Drosophila buzzatii have been
analyzed for mtDNA restriction polymorphisms. Most of the mtDNA nucleotide
variation in original populations of NW Argentina can be explained by
intrapopulation diversity and only a small fraction can be accounted for by
between-population diversity. Similar results are obtained using either the
estimated number of nucleotide substitutions per site or considering each
restriction site as a locus. Colonizer populations of the Iberian Peninsula
are monomorphic and show only the most common haplotype from the original
populations. Under the infinite island model and assuming that populations
are in equilibrium, fixation indices indicate enough gene flow to explain
why the populations are not structured. Yet, the possibility exists that
populations have not reached an equilibrium after a founder event at the
end of the last Pleistocene glaciation. Tajima's test suggests that
directional selection and/or a recent bottleneck could explain the present
mtDNA differentiation. Considering the significant population structure
found for the chromosomal and some allozyme polymorphisms, the among-
population uniformity for mtDNA variability argues in favor of the
chromosomal and some allozyme polymorphisms being adaptive.
相似文献
88.
Ganoderma microsporum immunomodulatory protein induces apoptosis and potentiates mitomycin C‐induced apoptosis in urinary bladder urothelial carcinoma cells
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89.
Monophyly of the order Rodentia inferred from mitochondrial DNA sequences of the genes for 12S rRNA, 16S rRNA, and tRNA-valine 总被引:3,自引:2,他引:1
A recent analysis of amino acid sequence data (Graur et al.) suggested that
the mammalian order Rodentia is polyphyletic, in contrast to most
morphological data, which support rodent monophyly. At issue is whether the
hystricognath rodents, such as the guinea pig, represent an independent
evolutionary lineage within mammals, separate from the sciurognath rodents.
To resolve this problem, we sequenced a region (2,645 bp) of the
mitochondrial genome of the guinea pig containing the complete 12S
ribosomal RNA, 16S ribosomal RNA, and transfer RNA(VAL) genes for
comparison with the available sciurognath and other mammalian sequences.
Several methods of analysis and statistical tests of the data all show
strong support for rodent monophyly (91%-98% bootstrap probability, or BP).
Calibration with the mammalian fossil record suggests a Cretaceous date
(107 mya) for the divergence of sciurognaths and hystricognaths. An older
date (38 mya) for the controversial Mus- Rattus divergence also is
supported by these data. Our neighbor-joining analyses of all available
sequence data (25 genes) confirm that some individual genes support rodent
polyphyly but that tandem analysis of all data does not. We propose that
the conflicting results are due to several compounding factors. The unique
biochemical properties of some hystricognath metabolic proteins, largely
responsible for generating this controversy, may have a single explanation:
a cascade effect resulting from inactivation of the zinc-binding abilities
of insulin. After excluding six genes possibly affected by insulin
inactivation, analyses of all available sequence data (7,117 nucleotide
sites, 3,099 amino acid sites) resulted in strong support for rodent
monophyly (94% BP for DNA sequences, 90% for protein sequences), which
lends support to the insulin-cascade hypothesis.
相似文献
90.
Nazeh M. Al-Abd Zurainee Mohamed Nor Marzida Mansor MS Hasan Mustafa Kassim 《The Korean journal of parasitology》2016,54(3):273-280
We evaluated the activity of methanolic extracts of Melaleuca cajuputi flowers against the filarial worm Brugia pahangi and its bacterial endosymbiont Wolbachia. Anti-Wolbachia activity was measured in worms and in Aedes albopictus Aa23 cells by PCR, electron microscopy, and other biological assays. In particular, microfilarial release, worm motility, and viability were determined. M. cajuputi flower extracts were found to significantly reduce Wolbachia endosymbionts in Aa23 cells, Wolbachia surface protein, and microfilarial release, as well as the viability and motility of adult worms. Anti-Wolbachia activity was further confirmed by observation of degraded and phagocytized Wolbachia in worms treated with the flower extracts. The data provided in vitro and in vivo evidence that M. cajuputi flower extracts inhibit Wolbachia, an activity that may be exploited as an alternative strategy to treat human lymphatic filariasis. 相似文献