Margareta Ackerman,Daniel G Brown,David Loker
Margareta Ackerman
Users of phylogenetic methods require rooted trees, because the direction of time depends on the placement of the root. While phylogenetic trees are typically rooted by using an out-group, this mechanism is inappropriate when the addition o...
Accuracy and efficiency of algorithms for the demarcation of bacterial ecotypes from DNA sequence data [0.03%]
用于根据DNA序列数据划分细菌生态型的算法的准确性和效率
Juan Carlos Francisco,Frederick M Cohan,Danny Krizanc
Juan Carlos Francisco
Identification of closely related, ecologically distinct populations of bacteria would benefit microbiologists working in many fields including systematics, epidemiology and biotechnology. Several laboratories have recently developed algori...
Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps [0.03%]
寻找重复序列——作为广义Ruzzo-Tompa算法用于带空隙的最佳子序列搜索示例问题研究
John L Spouge,Leonardo Mariño-Ramírez,Sergey L Sheetlin
John L Spouge
Some biological sequences contain subsequences of unusual composition; e.g. some proteins contain DNA binding domains, transmembrane regions and charged regions, and some DNA sequences contain repeats. The linear-time Ruzzo-Tompa (RT) algor...
Shibdas Bandyopadhyay,Sartaj Sahni,Sanguthevar Rajasekaran
Shibdas Bandyopadhyay
We propose a new algorithm, PMS6, for the (l,d)-motif discovery problem in which we are to find all strings of length l that appear in every string of a given set of strings with at most d mismatches. The run time ratio PMS5/PMS6, where PMS...
Junjie Li,Sanjay Ranka,Sartaj Sahni
Junjie Li
We develop novel single-GPU parallelisations of the Smith-Waterman algorithm for pairwise sequence alignment. Our algorithms, which are suitable for the alignment of a single pair of very long sequences, can be used to determine the alignme...
Fast decision tree-based method to index large DNA-protein sequence databases using hybrid distributed-shared memory programming model [0.03%]
基于快速决策树的索引大型DNA-蛋白质序列数据库的方法及混合分布共享内存编程模型
Khalid Mohammad Jaber,Rosni Abdullah,Nur&#x;Aini Abdul Rashid
Khalid Mohammad Jaber
In recent times, the size of biological databases has increased significantly, with the continuous growth in the number of users and rate of queries; such that some databases have reached the terabyte size. There is therefore, the increasin...
Monther Aldwairi,Bashar Al-Hajasad,Yaser Khamayseh
Monther Aldwairi
Finding the secondary structures of ribonucleic acid sequences is a very important task. The secondary structure helps determine their functionalities which in turn plays a role in the proteins production. Manual laboratory methods use X-ra...
Mo-Li Huang,Songsak Wattanachaisaereekul,Yu-Jun Han et al.
Mo-Li Huang et al.
Transposable Elements (TEs) play important roles in the evolution of eukaryotic organisms. TEs widely distribute depending on their properties present in the genome. This study elucidated the molecular characteristics of TEs in land plants ...
Tools, resources and databases for SNPs and indels in sequences: a review [0.03%]
序列中SNP和短片段缺失或插入的资源、工具和数据库综述
Abhik Seal,Arun Gupta,M Mahalaxmi et al.
Abhik Seal et al.
Single Nucleotide Polymorphism (SNP) is a mutation where, a single base in the DNA differs from the usual base at that position. SNPs are the marker of choice in genetic analysis and also useful in locating genes associated with diseases. S...
Structure, evolution and virtual screening of NDM-1 strain from Kolkata [0.03%]
新德里金属β-内酰胺酶-1（NDM-1）菌株的结构、进化和虚拟筛选
Ganesh Chandra Sahoo,Mukta Rani,Yousuf Ansari et al.
Ganesh Chandra Sahoo et al.
β-lactam antibiotics are utilised to treat bacterial infection. β-lactamase enzymes (EC 3.5.2.6) are produced by several bacteria and are responsible for their resistance to β-lactam antibiotics like penicillin, cephamycins and carbapene...