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

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.

• Publication year

  2018

• Venue

  PeerJ

• Publication date

  2018-07-04

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.7717/peerj.5099PMID 30013827PMCID 6035725
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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