ArticleGenome biology2016
A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed.
- SAUTE: sequence assembly using target enrichment.BMC bioinformatics · 2021Article
- Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads.Nucleic acids research · 2019Article
- MetaSort untangles metagenome assembly by reducing microbial community complexity.Nature communications · 2017Article
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Authors and funding
3 authors.
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Abstract
Most gene prediction methods detect coding sequences from transcriptome assemblies in the absence of closely related reference genomes. Such methods are of limited application due to high transcript fragmentation and extensive assembly errors, which may lead to redundant or false coding sequence predictions. We present inGAP-CDG, which can construct full-length and non-redundant coding sequences from unassembled transcriptomes by using a codon-based de Bruijn graph to simplify the assembly process and a machine learning-based approach to filter false positives. Compared with other methods, inGAP-CDG exhibits a significant increase in predicted coding sequence length and robustness to sequencing errors and varied read length.
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Registered trials
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