ORFanage: By-reference ORF annotation

ORFanage is an ultra-efficient pseudo-alignment algorithm for annotating ORFs by maximizing similarity to reference proteins.

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Example

For each overlap ORFanage extends coordinates towards the 3’ and 5’ ends based on suitable parameters.

$ orfanage --reference genome.fasta --output output.gtf \
        --query query.gtf reference.gtf

ORFanage allows users to rapidly search and find ORFs on query transcripts. Users may apply the method to their experimental datasets to:

• Search for likely coding transcripts

• Discover novel protein variants

• Identify and quantify AS events involved in any observed changes to the protein sequnces

• Much more

The method can also be applied to correct available protein annotations at loci with additional reference data.

The User Guide

• Installation
  • BioConda
  • Using Pre-Built Binaries
  • Building from source
• ORFanage
  • Preparing input data
  • Annotating Transcripts with ORFanage
  • Output Formats
  • Description of some important options
  • References
• ORFcompare
  • Basic Usage
  • Output Format
  • Description of Options
  • Interpreting Results
  • Example Analysis
• File Formats
  • Re-Annotated GTF Output
  • ORFanage Stats Output (TSV)
  • ORFcompare Stats Output (TSV)
• Examples
  • Annotating Proteins in isoforms of UPK1A
  • References
• Contact
  • E-Mail Us
  • Submit Issues and Requests