Abstract
For Salvia miltiorrhiza, bioinformatic tools have been used to analyze its DNA sequences, protein sequences as well as next-generation DNA sequencing (NGS) data studying the transcriptome, circular RNAs, etc. Here, we first described the basic file formats used in studying S. miltiorrhiza. FASTA is the standard format describing nucleotide and amino acid sequences. FASTQ format adds the quality scores to the FASTA file. GFF/GTF is used to describe the genome and gene structures, such as genes, CDS, proteins, exons, and introns. SAM format is widely used to describe the mapping of NGS reads to the reference sequences. For various analysis tasks, many commercial software tools have been developed. However, for users who prefer to use free software tools or develop computational pipelines, the basic function of EMBOSS software is introduced. Mapping of reads to reference sequences is the most widely used method for analyzing NGS data, and we introduced several frequently used tools. Bowtie2 is one of the most widely used tools for read mapping. SAMtools can be used to analyze the mapping data. As an example, several software packages identifying circRNAs are described. This chapter thus provides an introduction to the most fundamental bioinformatic tools.
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Acknowledgements
This work has been supported by Chinese Academy of Medical Sciences, Innovation Funds for Medical Sciences (CIFMS) (2016-I2M-3-016, 2017-I2M-1-013) and National Natural Science Foundation of China (81872966).
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Wang, L., Liu, C. (2019). Bioinformatic Tools for Salvia miltiorrhiza Functional Genomics. In: Lu, S. (eds) The Salvia miltiorrhiza Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-24716-4_9
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DOI: https://doi.org/10.1007/978-3-030-24716-4_9
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