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91.
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92.
93.
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94.
95.
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
96.
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
97.
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
98.
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
99.
Lake Ichkeul in northern Tunisia is a Ramsar site, a MAB Biosphere Reserve and a UNESCO World Heritage Site. The system is one of the most important coastal wetlands in North Africa, especially as an over-wintering area for migratory birds, particularly Palaearctic waterfowl. The present study was aimed at diagnosing the status of fish species in Lake Ichkeul and documenting their annual and seasonal occurrence within the system. Fish samples were collected monthly at 22 sites from March 2011 to April 2012 using a variety of gears, including a dragnet, gillnet, trammelnet, frynet and beach-seine. Temperature and salinity measurements were taken at each site, while fishes were obtained from only 11 sites, representing mainly lacustrine stations. A total of 18 fish species belonging to 14 genera and 12 families were identified, with Mugilidae dominating with four species, followed by Syngnathidae with three species. This study represents a relative recovery in terms of fish species richness, since only 13 species were recorded here between 2003 and 2007. However, the numbers of fish caught, especially of the commercial taxa, seem to have declined in recent years, and the number of species currently present is much lower than that of several decades ago. Increasing human pressures, particularly reductions in catchment freshwater inputs, a breakdown in ecosystem connectivity, pollution and over-fishing appear to be the principal causes for the decline in fish abundance and diversity. 相似文献
100.
黑长臂猿(Hylobates concolor)对人类和非人类捕食者的回避行为 总被引:6,自引:0,他引:6
捕食和避免捕在动物生存和进化过程中起着重要作用,本文报道了我们自1990年3月至1992年元月观察黑长臂猿对人类和非人类捕食者的一系列反映,在遇到人类(观察者)后,据离观察者的远近和受惊程度不同,它们表现出5种回避方式,而在遇到非人类捕食者时,成年雌雄性一起将捕食者引开,以保护其后代个体免遭捕食。文中还对这些不同的行为方式进行了讨论。成年雄性是群体的主要保护者,成年雌性在群体保护中也起到重要的作用 相似文献