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. (optional) InterProScan (methods: TIGRFAM, ProDom, SMART,  SUPERFAMILY, PANTHER, Gene3D, PIRSF, Pfam, Coils) 
4. Assignment of phytozome gene family (using HMMer)
5. Best-hit extraction by AHRD (Automated Human Readable Descriptions)

Results include: Phytozome gene family, AHRD descriptor, best BLAST hits, GO and InterPro ID (the latter two
only if InterProScan is run). 
Complete output files for each analysis are also provided. 

Note that the phytozome gene families which are searched are a subset of the phytozome v10.2 families. 
These are the families displayed on LIS, i.e., those having at least one member which is an LIS species.