Software for Automated Editing of Genome Sequences and Annotations

SeqNinja is a convenient tool for automated and batch editing of genome sequences and annotations. SeqNinja supports a variety of input/output file types for your projects, including FASTA files, GenBank files, and DNASTAR Lasergene files, and quickly converts sequences from one format to another. SeqNinja makes it easy for you to batch edit and export annotations, merge and split sequence data, and transfer annotations between genome versions, automating the process of adjusting sequence coordinates between assemblies. SeqNinja provides you with a variety of templates for common functions, as well as the ability to infinitely customize your projects.

Features & Highlights


Powerful Toolkit for Automated Genome Editing

  • Concatenate the generated contigs from a de novo SeqMan NGen assembly for ease of use in downstream analysis.
  • Copy annotations from a known sequence to an unannotated, but closely related sequence with SeqNinja's annotation mapping feature.
  • Correct large sequences by inserting or substituting bases. SeqNinja will adjust the annotation coordinates automatically.
  • Circularly permute a sequence within a gene of interest so that it is linearized at a different location.
  • Locate all genes annotated with a specified value or property.
  • Extract a set of annotated features from a genome and save them as protein or nucleotide sequences.


Streamlined Processing of Large Sequence Data Sets

  • Generate a multi-sequence FASTA file by extracting features, generating a reverse complement of your sequences, or translating a GenBank file.
  • Create custom sequence sets based on sequence names or patterns, and then use the resulting sets as the source for downstream operations such as feature extractions.
  • Sample sequences at random or based on user-defined criteria from large, multi-sequence files.
  • Use MegAlign Pro to run SeqNinja scripts and align resulting sequences directly.