SeqEditor

SeqEditor performs management, analysis, and curation of nucleotide and protein sequences to support primer design, sequence editing, annotation visualization (GTF/GFF), and inference of sequence metrics.

Key Features:

• Sequence Management: Handles large-scale genomic data including contigs, scaffolds, and entire chromosomes up to 300 megabases.
• GTF/GFF Viewer: Integrates a GTF/GFF file viewer for visualization and management of genome and transcriptome annotation files.
• Primer Design Tools: Provides utilities for singleplex and multiplex PCR primer design and employs a newly optimized and validated search strategy to identify target-specific and species-specific primers.
• Sequence Editing and Translation: Supports editing of nucleotide and protein sequences and translation of nucleotide sequences into proteins.
• ORF and Motif Search: Supports searching and filtering of sequences, open reading frames (ORFs), and sequence motifs.
• Multi-File Management: Manages multiple sequence and annotation files simultaneously for large-scale projects.
• Metrics Inference: Infers various sequence metrics to aid quantitative analysis of sequence data.

Scientific Applications:

• Genomic Research: Curation and annotation of genomic data including large chromosomes, contigs, and scaffolds.
• Transcriptomics: Management and analysis of transcriptome assemblies and associated GTF/GFF annotations.
• Diagnostic Development: Design of target-specific and species-specific primers for diagnostic PCR assays, including singleplex and multiplex formats.

Methodology:

Implemented in Java using the Eclipse Rich Client Platform; primer design uses a newly optimized and validated search strategy as stated in the source description.