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

Ahmed Hafez, Ricardo Futami, Amir Arastehfar, Farnaz Daneshnia, Ana Miguel, Francisco J Roig, Beatriz Soriano, Jaume Perez-Sánchez, Teun Boekhout, Toni Gabaldón, Carlos Llorens

Research output: Contribution to journal/periodicalArticleScientificpeer-review

5 Citations (Scopus)

Abstract

SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface (GIU) 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 data sets.

AVAILABILITY: SeqEditor was developed in Java using Eclipse Rich Client Platform and is publicly available at https://gpro.biotechvana.com/download/SeqEditor as binaries for Windows, Linux and Mac OS. The user manual and tutorials are available online at https://gpro.biotechvana.com/tool/seqeditor/manual.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original languageEnglish
JournalBioinformatics
DOIs
Publication statusPublished - 18 Oct 2020

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