Annotate a New Genome

The inputs are mostly self-evident, you pretty much just need to provide your assembled genome in fasta format to run the annotator. No "N"s in the fasta file was allowed at this time.

General information

Project Name -
Species Name -
Select input file in Fasta format. A sample file can be downloaded. -
Optionally, if you would like to receive a notification when the annotation is completed, please enter your email address -

Protein Identification

Select appropriate codon table -
Cutoff for Blastn E-value -
Cutoff for Blastx E-value -
Number of top hits to be included in the reference gene sets for annotation after the pre-filtering step -
Use repeatMasker -

tRNA Identification

Running aragorn -
Running tRNA-scan -
Search Mode -
Source -
Cutoff score (in bits) for reporting tRNAs -
set max length of tRNA intron+variable region -bp
Disable pseudo gene checking -

Repeat identification

Repeat Type
Search Parameters
1. Microsatelite Sequence Repeats -
2. Tandem Repeats -
3. Dispersed Repeats -

SNP Discovery (Optional)

Select input file in Fastq format. A tarred and gzipped sample file can be downloaded. -

RNA-editing Site Discovery (Optional)

Select input file in Fastq format. A tarred and gizipped sample file can be downloaded. -

Last updated: January 2nd, 2019.
For questions and comments, please send email to or

Center for Bioinformatics
Institute of Medicinal Plant Development
PeKing Union Medical College
Chinese Academy of Medical Sciences
Address: No. 151, Malianwa North Road, Haidian District, Beijing 100093, P.R.China