Since transcriptome analysis provides genome-wide sequence and gene expression information, transcript reconstruction using RNA-Seq sequence reads has become popular during recent years. For non-model organism, as distinct from the reference genome-based mapping, sequence reads are processed via de novo transcriptome assembly approaches to produce large numbers of contigs corresponding to coding or non-coding, but expressed, part of genome. In spite of immense potential of RNA-Seq–based methods, particularly in recovering full-length transcripts and spliced isoforms from short-reads, the accurate results can be only obtained by the procedures to be taken in a step-by-step manner. In this chapter, we aim to provide an overview of the state-of-the-art methods including (i) quality check and pre-processing of raw reads, (ii) the pros and cons of de novo transcriptome assemblers, (iii) generating non-redundant transcript data, (iv) current quality assessment tools for de novo transcriptome assemblies, (v) approaches for transcript abundance and differential expression estimations and finally (vi) further mining of transcriptomic data for particular biological questions. Our intention is to provide an overview and practical guidance for choosing the appropriate approaches to best meet the needs of researchers in this area and also outline the strategies to improve on-going projects.
Part of the book: Applications of RNA-Seq and Omics Strategies
DNA, as a natural biological nanowire, could be modified by inorganic atoms, either conducting or semi‐conducting ones, to render feasible for technological applications and sequencing. Magnetic phase transition of modified DNA (M‐DNA) nanowire, similar to diluted magnetic semiconductor (DMS) materials, occurs by changing parameters such as temperature and doping ratio having critical values. Tuning such parameters provide a pleasant control about determination of the magnetic property of M‐DNA, particularly room‐temperature soft ferromagnetism. In this chapter, a fundamental theory for anti‐ferromagnetic Cr3+‐doped M‐DNA nanowire named as diluted magnetic organic structures (DMOS) is tried to figure out the interactions representing the exotic behaviour of these type of organometallics. However, authors detailed preparation of nanowire as a global input and overall procedure of simulation based on Markov chain Monte Carlo (MCMC) method.
Part of the book: Nanowires