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Bayesian adaptive sequence alignment algorithms 总被引:3,自引:1,他引:2
The selection of a scoring matrix and gap penalty parameters continues to
be an important problem in sequence alignment. We describe here an
algorithm, the 'Bayes block aligner, which bypasses this requirement.
Instead of requiring a fixed set of parameter settings, this algorithm
returns the Bayesian posterior probability for the number of gaps and for
the scoring matrices in any series of interest. Furthermore, instead of
returning the single best alignment for the chosen parameter settings, this
algorithm returns the posterior distribution of all alignments considering
the full range of gapping and scoring matrices selected, weighing each in
proportion to its probability based on the data. We compared the Bayes
aligner with the popular Smith-Waterman algorithm with parameter settings
from the literature which had been optimized for the identification of
structural neighbors, and found that the Bayes aligner correctly identified
more structural neighbors. In a detailed examination of the alignment of a
pair of kinase and a pair of GTPase sequences, we illustrate the
algorithm's potential to identify subsequences that are conserved to
different degrees. In addition, this example shows that the Bayes aligner
returns an alignment-free assessment of the distance between a pair of
sequences.
相似文献
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Lemberger KY Gondim LF Pessier AP McAllister MM Kinsel MJ 《The Journal of parasitology》2005,91(4):960-961
During a canine distemper virus (CDV) outbreak in raccoons (Procyon lotor) from Cook County, Illinois, a juvenile female suffering from seizures was killed and necropsied. Gross and histologic findings of necrotizing encephalitis and proliferative bronchopneumonia were attributed to CDV infection and considered the cause of clinical signs. A section of cerebellum stained immunohistochemically for Neospora caninum revealed an approximately 40 microm diameter, round to oval cyst with a 2- to 3-microm-thick wall and filled with 1-2 microm diameter, round to oval bradyzoites. Polymerase chain reaction (PCR) results were positive for N. caninum using DNA extracted from the brain. Specific PCR for the closely related organisms Toxoplasma gondii and Hammondia heydorni yielded negative results. This case report provides histologic, immunohistochemical, and molecular evidence that raccoons are a naturally occurring intermediate host of N. caninum. 相似文献
56.
Casanova E Fehsenfeld S Lemberger T Shimshek DR Sprengel R Mantamadiotis T 《Genesis (New York, N.Y. : 2000)》2002,34(3):208-214
Here we describe the generation of a new tamoxifen-inducible double Cre fusion protein generated by fusing two ERT2 domains onto both ends of the iCre recombinase (a codon improved Cre recombinase). This Cre fusion protein (ERiCreER) had a twofold increased activity in cell culture assays than the previously described MerCreMer Cre double fusion protein. ERiCreER was targeted to the brain by placing it under the control of the promoter from the CamKIIalpha gene using a 170 kb BAC. The fusion protein was detected in hippocampus, cortex, striatum, thalamus, and hypothalamus but not in cerebellum. The ERiCreER was cytoplasmatic in the absence of tamoxifen and translocated into the nucleus upon tamoxifen administration. The activity of the ERiCreER was tested in vivo by mating the CamKIIalpha ERiCreER transgenic line with mice harbouring exon 10 of the CREB gene flanked by two LoxP sites. In the absence of tamoxifen, no background activity was detected in mice older than 6 months. After tamoxifen administration, most if not all of the ERiCreER fusion protein translocated from the cytoplasm to the nucleus; however, only 5-10% of the "floxed" CREB allele was recombined. Recombination was also visualised at the cellular level by following the upregulation of the CREM protein, which corresponds precisely with CREB loss/recombination. Unlike in other tissues (Sohal et al., 2001; Tannour-Louet et al., 2002), it appears that in brain, although ERiCreER can bind tamoxifen, the Cre-recombinase cannot be fully activated. 相似文献
57.
Casanova E Lemberger T Fehsenfeld S Mantamadiotis T Schütz G 《Genesis (New York, N.Y. : 2000)》2003,37(1):25-29
The Cre-loxP system is increasingly exploited for spatial and temporal gene inactivation. Here we present a novel approach to achieve this goal of selective gene inactivation. Following the model of alpha complementation in the beta-galactosidase enzyme, where the enzyme is split into independent polypeptides which are able to associate and maintain the enzymatic activity, we divided the Cre recombinase into two independent polypeptides (one containing the NH(2) terminus (alpha) and a second one containing the COOH-terminus (beta)). Individually, the two polypeptides have no detectable activity. However, when coexpressed the polypeptides are able to associate, giving rise to Cre enzymatic activity, which optimally is as high as 30% of that seen with wildtype Cre recombinase in vitro. We present this strategy as a modification of the traditional Cre-loxP system, which could be used to obtain a highly specific recombination pattern by expressing the two halves under the control of separate promoters. 相似文献
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Ingolf Sommer Stefano Toppo Oliver Sander Thomas Lengauer Silvio CE Tosatto 《BMC bioinformatics》2006,7(1):364
Background
In the area of protein structure prediction, recently a lot of effort has gone into the development of Model Quality Assessment Programs (MQAPs). MQAPs distinguish high quality protein structure models from inferior models. Here, we propose a new method to use an MQAP to improve the quality of models. With a given target sequence and template structure, we construct a number of different alignments and corresponding models for the sequence. The quality of these models is scored with an MQAP and used to choose the most promising model. An SVM-based selection scheme is suggested for combining MQAP partial potentials, in order to optimize for improved model selection. 相似文献60.