Comparative modeling of coevolution in communities of unicellular organisms: adaptability and biodiversity [0.03%]
单细胞生物种群中共进化比较模型的研究：适应性和多样性
Sergey A Lashin,Valentin V Suslov,Yuri G Matushkin
Sergey A Lashin
We propose an original program "Evolutionary constructor" that is capable of computationally efficient modeling of both population-genetic and ecological problems, combining these directions in one model of required detail level. We also pr...
Valentin V Suslov,Petr M Ponomarenko,Vadim M Efimov et al.
Valentin V Suslov et al.
Evolutionary trends have been examined in 146 HIV-1 forms (2662 copies, 2311 isolates) polymorphic for the TATA box using the "DNA sequence-->affinity for TBP" regression (TBP is the TATA binding protein). As a result, a statistically signi...
Computational approaches for drug repositioning and combination therapy design [0.03%]
用于药物再定位和联合用药设计的计算方法
Ekaterina Kotelnikova,Anton Yuryev,Ilya Mazo et al.
Ekaterina Kotelnikova et al.
Heterogeneous high-throughput biological data become readily available for various diseases. The amount of data points generated by such experiments does not allow manual integration of the information to design the most optimal therapy for...
Statistical comparison of methods to estimate the error probability in short-read Illumina sequencing [0.03%]
短读 illumina 测序估计错误概率方法的统计比较
Irina Abnizova,Tom Skelly,Fedor Naumenko et al.
Irina Abnizova et al.
As was the case in the beginning of the sequencing era, the new generation of short-read sequencing technologies still requires both accuracy of data processing methods and reliable measures of that accuracy. Inspired by the classic of the ...
Probe-Level Universal Search (PLUS) algorithm for gender differentiation in affymetrix datasets [0.03%]
探针层面的万用搜索(PLUS)算法在Affymetrix数据集中进行性别区分
Anna S Karyagyna,Michail O Vassiliev,Anna S Ershova et al.
Anna S Karyagyna et al.
Affymetrix microarrays measure gene expression based on the intensity of hybridization of a panel of oligonucleotide probes (probe set) with mRNA. The signals from all probes within a probe set are converted into a single measure that repre...
Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm [0.03%]
基因特追迹：利用维特比算法识别蛋白质编码序列中的移码突变
Ivan Antonov,Mark Borodovsky
Ivan Antonov
We describe a new program for ab initio frameshift detection in protein-coding nucleotide sequences. The task is to distinguish the same strand overlapping ORFs that occur in the sequence due to a presence of a frameshifted gene from the sa...
Sergey I Mitrofanov,Alexander Y Panchin,Sergei A Spirin et al.
Sergey I Mitrofanov et al.
We studied the distribution of 1-7 bp words in a dataset that includes 139 complete eukaryotic genomes, 33 masked eukaryotic genomes and coding regions from 35 genomes. We tested different statistical models to determine over- and under-rep...
Malakite: an automatic tool for characterisation of structure of reliable blocks in multiple alignments of protein sequences [0.03%]
用于蛋白质序列多重联配中可靠块结构特征的自动工具malakite
Boris Burkov,Boris Nagaev,Sergei Spirin et al.
Boris Burkov et al.
It makes sense to speak of alignment of protein sequences only within the regions, where the sequences are related to each other. This simple consideration is often disregarded by programs of multiple alignment construction. A package for a...
A parallel scheme for comparing transcription factor binding sites matrices [0.03%]
转录因子结合位点矩阵的并行比较方案
Solenne Carat,Rémi Houlgatte,Jérémie Bourdon
Solenne Carat
Gene regulation implies many mechanisms. Their identification is a crucial task to construct regulatory networks, and is necessary to understand the pathology in many cases. This requires the identification of transcription factors that pla...