Sequence and Structure Analysis of Biological Molecules Based on Computational Methods

Jia-Feng Yu, Yue-Dong Yang, Xiao Sun, Ji-Hua Wang
2015 BioMed Research International  
The number of sequences and structures of biological molecules, such as DNA, RNA, and proteins, is rapidly increasing in databases. According to the statistics in the newest version of GOLD database (https://gold.jgi-psf.org/) [1], 6651 genomes have been completed and published and 51954 genomes are of permanent drafts or incomplete. The protein data bank (PDB, http://www.rcsb.org/) [2] has published 107958 biological macromolecular structures, including 35542 protein sequences, 28142
more » ... of human sequences, and 7611 nucleic acid containing structures. To discover the underlying mechanism behind the information, it is necessary to develop effective feature parameters for representing the sequence and structure. Although many studies have been proposed for sequence and structure analysis, more and more studies indicated that the problem is far from solved [3, 4] . How to computationally analyze the big data of biologically molecular sequences and structures has been one of the major challenges in bioinformatics. Machine learning and optimization methods are important methods for the analyses. This special issue focuses on recent progress of the computational methods for biological sequences or structures studies. Correspondingly, after a rigorous peer review, eleven papers were selected. We briefly describe these papers as follows. In "Predicting Homogeneous Pilus Structure from Monomeric Data and Sparse Constraints, " K. Xiao et al. developed a new approach to predict pseudoatomic models of pili by combining ambiguous symmetric constraints with sparse distance information obtained from experiments. The method was successfully implemented to the reconstruct the gonococcal (GC) pilus from Neisseria gonorrhoeae. A global sampling in a wide range implied that a pilus might have more than one but fewer than many possible intact conformations. In "Evolutionary and Expression Analysis of miR-#-5p and miR-#-3p at the miRNAs/isomiRs Levels, " L. Guo et al. explored the potential evolutionary and expression divergence and relationships between miRNAs from different arms of different/same pre-miRNAs according to the arm selection and/or arm switching phenomenon in miRNA world. They found no bias in the numbers but different nucleotide compositions between 5p-miRNA and 3p-miRNA. IsomiR expression profiles from the two arms are always stable, but isomiR expressions in diseased samples are prone to show larger degree of dispersion. miR-#-5p and miR-#-3p have relative independent evolution/expression patterns and datasets of target mRNAs, which might also contribute to the phenomena of arm selection and/or arm switching. Simultaneously, miRNA/isomiR expression profiles may be regulated via arm selection and/or arm switching, and the dynamic miRNAome and isomiRome will adapt to functional and/or evolutionary pressures. A comprehensive analysis and further experimental study at the miRNA/isomiR levels are quite necessary for miRNA study.
doi:10.1155/2015/565328 pmid:26236729 pmcid:PMC4506833 fatcat:f4yu6c4vrjbaxigs4d326452ey