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

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

SUBMITTER: Camiolo S 

PROVIDER: S-EPMC6035725 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature