ArticleGenes & genomics2023
StringFix: an annotation-guided transcriptome assembler improves the recovery of amino acid sequences from RNA-Seq reads.
Article in Genes & genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundReconstruction of amino acid sequences from assembled transcriptome is of interest in personalized medicine, for example, to predict drug-target (or protein-protein) interaction considering individual's genomic variations. Most of the existing transcriptome assemblers, however, seems not well suited for this purpose.
methodsIn this work, we present StringFix, an annotation guided transcriptome assembly and protein sequence reconstruction software tool that takes genome-aligned reads and the annotations associated to the reference genome as input. The tool 'fixes' the pre-annotated transcript sequence by taking small variations into account, finally to produce possible amino acid sequences that are likely to exist in the test tissue.
resultsThe results show that, using outputs from existing reference-based assemblers as the input GTF-guide, StringFix could reconstruct amino acid sequences more precisely with higher sensitivity than direct generation using the recovered transcripts from all the assemblers we tested.
conclusionBy using StringFix with the existing reference-based assemblers, one can recover not only a novel transcripts and isoforms but also the possible amino acid sequence stemming from them.
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