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91.
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92.
Mechanisms of selection for drought stress tolerance and avoidance in Impatiens capensis (Balsaminaceae) 总被引:2,自引:0,他引:2
For longer lived annual plants, high water-use efficiency (WUE) and low stomatal conductance are hypothesized to confer a fitness advantage under drought stress. To directly test the adaptive significance of WUE and stomatal conductance under drought stress, inbred lines of Impatiens capensis were grown in two field environments (watered and not-watered), in a year of unusual early-season drought. In contrast to the results from a previous study of late-season drought in the same system, selection was detected for lower WUE, increased stomatal conductance, and early flowering time. These findings suggest that early-season drought conditions may select for drought avoidance traits such as low WUE and early reproduction, whereas later drought selects for tolerance traits such as high WUE. 相似文献
93.
Evidence of adaptive divergence in plasticity: density- and site-dependent selection on shade-avoidance responses in Impatiens capensis 总被引:1,自引:0,他引:1
Donohue K Messiqua D Pyle EH Heschel MS Schmitt J 《Evolution; international journal of organic evolution》2000,54(6):1956-1968
We investigated the conditions under which plastic responses to density are adaptive in natural populations of Impatiens capensis and determined whether plasticity has evolved differently in different selective environments. Previous studies showed that a population that evolved in a sunny site exhibited greater plasticity in response to density than did a population that evolved in a woodland site. Using replicate inbred lines in a reciprocal transplant that included a density manipulation, we asked whether such population differentiation was consistent with the hypothesis of adaptive divergence. We hypothesized that plasticity would be more strongly favored in the sunny site than in the woodland site; consequently, we predicted that selection would be more strongly density dependent in the sunny site, favoring the phenotype that was expressed at each density. Selection on internode length and flowering date was consistent with the hypothesis of adaptive divergence in plasticity. Few costs or benefits of plasticity were detected independently from the expressed phenotype, so plasticity was selected primarily through selection on the phenotype. Correlations between phenotypes and their plasticity varied with the environment and would cause indirect selection on plasticity to be environment dependent. We showed that an appropriate plastic response even to a rare environment can greatly increase genotypic fitness when that environment is favorable. Selection on the measured characters contributed to local adaptation and fully accounted for fitness differences between populations in all treatments except the woodland site at natural density. 相似文献
94.
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95.
96.
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
97.
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
98.
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
99.
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
100.
Ganoderma microsporum immunomodulatory protein induces apoptosis and potentiates mitomycin C‐induced apoptosis in urinary bladder urothelial carcinoma cells 下载免费PDF全文