SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files

[Motivation]: Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user’s expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences’ analysis.
[Result]: SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface and can work either as a graphical sequence browser or as a fasta task manager for multi-fasta files. SeqEditor has been optimized for the management of large sequences, such as contigs, scaffolds or even chromosomes, and includes a GTF/GFF viewer to visualize and manage annotation files. In turn, this allows for content mining from reference genomes and transcriptomes with similar efficiency to that of command line tools. SeqEditor also incorporates a set of tools for singleplex and multiplex PCR primer design and pooling that uses a newly optimized and validated search strategy for target and species-specific primers. All these features make SeqEditor a flexible application that can be used to analyses complex sequences, design primers in PCR assays oriented for diagnosis, and/or manage, edit and personalize reference sequence datasets.
This work was supported by the European Union’s Horizon 2020 Research and Innovation programme under the Marie Sklodowska-Curie grant agreement [642095] of the OPATHY consortium; by the pre-doctoral research fellowship from Industrial Doctorates of MINECO [DI-17-09134]; and by the State Plan for Scientific and Technical Research and Innovation 2017-2020 of the Secretary of State for Digital Advancement of Ministry of Economic Affairs and Digital Transformation, Spain [TSI-100903-2019-11].