corseq: fast and efficient identification of favoured codons from next generation sequencing reads

Clicks: 168
ID: 249979
2018
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Abstract
Background Optimization of transgene expression can be achieved by designing coding sequences with the synonymous codon usage of genes which are highly expressed in the host organism. The identification of the so-called “favoured codons” generally requires the access to either the genome or the coding sequences and the availability of expression data. Results Here we describe corseq, a fast and reliable software for detecting the favoured codons directly from RNAseq data without prior knowledge of genomic sequence or gene annotation. The presented tool allows the inference of codons that are preferentially used in highly expressed genes while estimating the transcripts abundance by a new kmer based approach. corseq is implemented in Python and runs under any operating system. The software requires the Biopython 1.65 library (or later versions) and is available under the ‘GNU General Public License version 3’ at the project webpage https://sourceforge.net/projects/corseq/files. Conclusion corseq represents a faster and easy-to-use alternative for the detection of favoured codons in non model organisms.
Reference Key
camiolo2018peerjcorseq: Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Salvatore Camiolo;Andrea Porceddu
Journal pediatrics
Year 2018
DOI
10.7717/peerj.5099
URL
https://peerj.com/articles/5099/
Keywords
preferred codonsmedicine

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