Transcript Annotation

Upload a file of protein or nucleotide sequences and have them annotated using LIS legume resources.

Because this service involves several computationally-intensive searches
(see pipeline description below), results can take from several minutes to
several hours, depending on the size of your query. Thanks for your patience.


Annotation pipeline:

1. ESTScan if needed (to translate nucleotide uploads)
2. BLAST alignment to reference gene databases (Soy, Medicago, Arabidopsis)
3. InterProScan (methods: TIGRFAM, ProDom, SMART, ProSiteProfiles, ProSitePatterns, SUPERFAMILY, PANTHER, Gene3D, PIRSF, Pfam, Coils) 
4. Assignment of phytozome gene family (using HMMer)
5. Best-hit extraction by AHRD (Automated Human Readable Descriptions)

Summary results provided including: GO, InterPro ID, Gene family, and AHRD descriptor.
Complete outputs of each analysis are also provided.