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

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PeerJ

PeerJ Inc.

Optimal codons, Codon bias, Transgene expression optimization, Preferred codons

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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.

      Related collections

      Most cited references 26

      • Record: found
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      Fast and accurate long-read alignment with Burrows–Wheeler transform

      Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.sourceforge.net Contact: rd@sanger.ac.uk
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        Biopython: freely available Python tools for computational molecular biology and bioinformatics

        Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_lists peter.cock@scri.ac.uk.
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          Synonymous but not the same: the causes and consequences of codon bias.

          Despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. Although recent advances in sequencing and synthetic biology have helped to resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts.
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            Author and article information

            Affiliations
            Dipartimento di Agraria, Università degli studi di Sassari , Sassari, Italy
            Contributors
            Journal
            PeerJ
            PeerJ
            peerj
            peerj
            PeerJ
            PeerJ Inc. (San Francisco, USA )
            2167-8359
            4 July 2018
            2018
            : 6
            6035725
            5099
            10.7717/peerj.5099
            (Editor)
            ©2018 Camiolo and Porceddu

            This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

            Funding
            The authors received no funding for this work.
            Categories
            Bioinformatics
            Biotechnology
            Computational Biology
            Genomics

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