In November 2016, the international academic journal Genome Biology published the latest research on the team of researcher Zhao Fangqing of the Computational Genomics Laboratory of the Beijing Institute of Biological Sciences, Chinese Academy of Sciences entitled "A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes". Results. This study proposes a new algorithm based on the codon de Bruijn graph, which uses the non-splicing strategy to directly encode and reconstruct the transcriptome sequencing data, which solves the problem of low and inefficient coding gene encoding. The field of biological evolutionary genome research has great application prospects.
In recent years, the rapid development of high-performance computing technology and high-throughput sequencing technology has facilitated the implementation of a large number of genome sequencing projects, resulting in massive bio-omics data. In the face of transcriptome data, scientists' primary task is to obtain their encoded gene information. Traditional gene recognition tools rely primarily on transcripts obtained from RNA-seq assembly software for genetic identification. One of the disadvantages of these tools is that the assembly software is highly sensitive to sequencing errors and does not effectively process repetitive sequence regions, thus resulting in gene recognition on the basis of which a large number of highly redundant and fragmented gene sequences are generated. In addition, these tools need to be overly dependent on homologous gene databases or reference genomes and cannot be effectively applied to gene recognition of transcriptome data from non-model species. Therefore, a new algorithm for reconstructing coding genes based on transcriptome data needs to be developed.
De Bruijn map based on transcriptome data (left) and genomic data (right)
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