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Multiple sequence alignment (MSA) methods infer the homologous regions within DNA and protein sequences. Among the other algorithms for MSA, the center star method (CSM) is useful when processing a large number of sequences. In this method, the partially conserved regions among the non-center sequences tend to hide in the alignment. Therefore, existence of subsets of similar sequences in the input...
DNA sequences consist of four types of nucleotides, and converting the DNA sequence into a numerical sequence is an important task of the study of DNA sequences. In this paper, we propose an improved inter-nucleotide distances method which combines with Euclidean distance to analyze phylogenetic relationship of the 64 vertebrate complete mitochondrial genomes and construct corresponding phylogenetic...
The auxin response factors are key regulators for growth and development of plant. In this study, a total of 32 BrARF genes that distributed on the ten chromosomes were identified in rape genome. ARF gene family of Rape is expanded as compared to the ARF genes of rice (25) and arabidopsis (23). Sequence alignment and phylogenetic analysis showed that some BrARF proteins fall into related sister pairs,...
A reconfigurable processor tailored for accelerating Phylogenetic Inference is proposed. In this paper, a programmable and scalable architectural platform instantiates an array of coarse grained light weight processing elements and allows arbitrary partitioning and scheduling schemes and capable of solving complete Maximum Likelihood algorithm and deal with arbitrarily large sequences. The key difference...
Multiple sequence alignment is a scientific tool to assist the study of DNA homology, phylogeny determinations, and conserved motifs identification. Various heuristic MSA methods have been presented to obtain the resulting alignment for multiple sequences. Although these alignment tools are able to align protein, DNA, and RNA sequences successfully, they are not such successful in aligning coding...
Likelihood-based reconstruction of phylogenetic (evolutionary) trees from molecular sequence data exhibits extreme resource requirements because of the high computational cost of the phylogenetic likelihood function. We propose a dedicated computer architecture for the inference of phylogenies under the maximum likelihood criterion. Our design is sufficiently generic to support any possible input...
The taxonomy of the large dsDNA viruses has been provided in the VIIIth report of ICTV. The phylogenetic tree of large dsDNA viruses has been constructed using CVTree method (Gao and Qi, BMC Evol. Biol.7(2007)41). In this paper, we use the log-correlation distance method analyze the complete genome of the 124 large dsDNA viruses and construct phylogenetic trees based on compositional vectors of DNA...
The partial sequence of the psbA gene from Cladosiphon okamuranus was amplified by PCR and their sequences were analysed. Neighbor-joining method was used to build phylogenetic trees according to the psbA sequence among 11 species, C. okamuranus included, that are affiliated to the algal order Ectocarpales. The results showed that the nucleotide sequence is 737 bp and the sequence shares high homology...
In the ABC model, MADs-box proteins play an important role in floral development. As one of the MADs-box proteins, PI behaves as B function organ-identity genes acting in the second and third whorls of the flower to control petal and stamen identity. To find genes involved in the floral transition of pineapple guava, we cloned the full length cDNA encoding a MADs-box protein in Coolidge pineapple...
Modification of histone proteins is associated with chromatin accessibility which profound epigenetic effect on DNA transcription, repair and replication. The SET domain proteins are recognized as regulating gene expression through lysine residues of histione methylation. Previous reports classified the SET domain proteins for 5 classes and 19 groups. In this study, we identified 15 barley SET domain...
Lipoprotein lipase (LPL) of Tianfu meat goose was cloned and sequenced using a RT-PCR approach. The nucleotide sequence covered 468 bp with an open reading frame of 155 amino acids. Alignment analysis indicated that the nucleotide sequences are highly conserved to other species studied including chicken, domestic guinea pig, house mouse, Norway rat, cattle, cow and goat, and the homologies are 92...
β-ketoacyl-ACP synthetase II (KAS II) which catalyzes the elongation of 16:0-ACP to 18:0-ACP, determines the ratio of palmitic acid (16:0) to stearic acid (18:0). Using Rapid Amplification of cDNA Ends (RACE) and a peanut cDNA library we had previously constructed, we isolated a 1867bp cDNA of the KAS II gene containing a 1212bp complete open reading fragment (ORF). Sequence analysis revealed that...
Kosteletzkya virginica is a halophyte species which could be used for production of industrial raw material such as biodiesel and for developing ecologically sound saline agriculture as well as for tideland soil improving. Using Rapid Amplification of cDNA Ends (RACE) method, a 1610 bp cDNA of stearoyl-ACP desaturase (SAD) gene containing a 1188 bp complete open reading fragment (ORF) was firstly...
With genome-wide screening of N. vectensis, two new groups of Polinton were identified, beside five Polinton groups deposited in Repbase. The typical N. vectensis Polinton is in length of 15-20kb and has long TIRs with a 6-bp TSDs. it encodes as many as 6 different proteins, including retroviral-like integrase (INT), adenovirus protease (PRO), DNA polymerase B (POLB) and putative ATPase (ATP). These...
DNA sequences are often found to be composed of locally homogeneous segments that are functionally important. Most sequence comparison methods do not consider such a compositional property. We introduce a new method that takes this issue into consideration. With our method, the information of a DNA sequence is first transformed into a multi-order transition matrix (MTM); the resulting matrices are...
It is important to develop computational methods to predict target genes of a transcription factor. In this paper, we developed a phylogenetic footprinting method to effectively identify target genes on the whole genome scale. Appling the method to 31 transcription factors, we improved the quality of the initial motifs, and predicted additional target genes that are supported by gene ontology analysis...
The emergence and spread of multidrug-resistant strains of Mycobacterium tuberculosis represent an increasing public health problem. Understanding multidrug-resistant mechanism(s) is essential for efficient treatment and control of tuberculosis. Mutations in gene rpsL, encoding the ribosomal protein S12, are responsible for most of the high-level Streptomycin resistance in Mycobacterium tuberculosis...
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