Annotate a New Genome

For the impatient (Apr. 24th, 2017)!
To run the annotator, you need to at least
(1) select the "plant" under "Taxon Group";
(2) select "all" from the refernece list;
(3) load you sequence in fasta format;
(4) click "submit".

The default parameters have been found to generate consistent results. Using other parameters might result in unexpected results. If you are not sure what you are doing, please use the default parameters.

General information

Project Name -
Taxon Group
Note, more taxon groups are to be added.
Species Name -
Select input file in Fasta format. A sample file can be downloaded. -
Output Image Format -
Optionally, if you would like to receive a notification when the annotation is completed, please enter your email address -

Blast related parameters

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 -

Select references

Select the minimal numbers of member genes/protein for a homologous group to be included as reference gene/protein sets for annotation -
Select the species you would like to be included as the reference for annotation. The default is all species. Note, if this box is blank, please specify the taxon group from above first. -

tRNA-scan related parameters

Search Mode -
Source -
Cutoff score (in bits) for reporting tRNAs -
set max length of tRNA intron+variable region -bp

Amino Acid Codon Table

Select appropriate codon table -

Last updated: July 15th, 2016.
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