It is the key link to apply high-performance computing to biology. In the research of bioinformatics ( Wang et al., 2015), biological sequence alignment is one of the important processes of similarity analysis between unknown and known molecular sequences, the basis of biological sequence analysis and database search, and used in the sequence assembly. A star alignment algorithm is designed and generated to demonstrate the development process.Īlignment is a common and important approach in biology study. Based on our constructed pairwise sequence alignment algorithm component library and the convenient software platform PAR, a few expansion domain components are developed for multiple sequence alignment application domain, and specific multiple sequence alignment algorithm can be designed, and its corresponding program, i.e., C++/Java/Python program, can be generated efficiently and thus enables the improvement of the development efficiency of complex algorithms, as well as accuracy of sequence alignment calculation. Multiple sequence alignment algorithms are more complex, redundant, and difficult to understand, and it is not easy for users to select the appropriate algorithm some computing errors may occur. Existing research focuses mainly on the specific steps of the algorithm or is for specific problems, lack of high-level abstract domain algorithm framework. 3School of Computer and Information Engineering, Jiangxi Normal University, Nanchang, ChinaĪs a key algorithm in bioinformatics, sequence alignment algorithm is widely used in sequence similarity analysis and genome sequence database search.2School of Software, Jiangxi Normal University, Nanchang, China.1School of Information Management, Jiangxi University of Finance and Economics, Nanchang, China.This is a direct consequence of its importance in the T cell proliferation pathway.Haipeng Shi 1,2, Haihe Shi 3 * and Shenghua Xu 1 To view the larger and more comprehensive phylogenetic tree, please visist the Phylogenetic Tree section.įrom this multiple sequnece alignment it is concluded that CaMKIV is highly conserved in evolution, mainly its four identified domains. This result will become more relevant when using the tool to make the phylogenetic tree using many more species. This result confirms the validity of the bioinformatics tool in the case of CaMKIV. It is therefore not necessarily representative of the phylogenetic distance between species.ĭespite this, the tree respects the general evolutionary relationship. This small phylogenetic tree was obtained with the COBALT or “ constraint-based alignment tool” on NCBI and is based on protein sequence data. This protein has been predicted using the Swissmodel (an automated protein modelling server), for more information please visit: However, thale cress differs the most, having a longer sequence than the other species, leading to deletions in the alignment. All four domains are exceptionally conserved amongst all the reference species. Note that the protein is a predicted model, whose sequence stops straight after the Calmodulin-Binding Domain. By the C-terminus of the helix, and of the protein, is the Calmodulin-Binding Domain (blue). At the N-terminus of such helix are the autoinhibitory Domain (magenta) and the PP2A-Binding Domain (cyan), which greatly overlap (depicted as different coloured overlapping dots). The catalytic domain (yellow) makes up almost all of the protein except for the autoinhibitory helix. Shown here all four highly conserved domains of CaMKIV. Scroll over the diagram below and click on the domains to be linked to their explanations. You can gain access to the relevant details of a specific domain by clicking anywhere within the corresponding coloured domain region in the diagram below. Including species which are phylogenetically very far highlights the parts of the protein which remained conserved throughtout evolution, which is a strong indicator of their importance (shown in image). Finally is thale cress (Arabidopsis thaliana), which belongs to a different kingdom. These are followed by chicken ( Gallus gallus), a bird, and by zebrafish ( Danio rerio), a fish, both being genetically more different to mammals. Then follow house mouse ( Mus musculus) and common rat ( Rattus novegicus), both being also mammals. At the top is human ( Homo Sapiens), followed by common chimpanzee ( Pan troglodytes), which is very closely related. Note that the species were arranged in the multiple sequence alignment according to their genetic similarities determined by the phylogenetic tree. Shown below are a multiple sequence alignment of seven different representative CaMKIV across different species their corresponding phylogenetic tree and an image of the protein's conserved domains.
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