MaizeGDB
jobs | upcoming events | sitemap
 | docs | bulk data | browse data | tools | login / register | links 
homeA popup window providing help for using the search form to the right  

Project Documentation & Protocols: Maize Gene Discovery Project: ESTs: Annotation

Contents: Index | Libraries | Reports | Assembly | Annotation | Unigene | Search | Ordering | Protocols | FAQs

Automatic annotation of the ZmDB sequences is currently done by searching GenPept using the NCBI Blastx program. Only hits with an E value smaller than 1e-10 are selected, corresponding to proteins with high degree of sequence similarity to the ZmDB sequence inferred translation products. Automatic annotation is aided by the program MuSeqBox (Multi-query SEQuence Blast Outout eXamination), developed in our group. For each query sequence, the top hits (if any) are selected and annotated as potential homologs of the inferred EST sequence. Keywords of these hits are also used as the keywords of the ZmDB sequence. This allows the ZmDB users to search the database by keyword for sequence of interest using either Text Search or ACE Query. Table Maker can be used to extract such information for all or a large batch of the ZmDB sequences. A link to the record of each hit at NCBI is provided.

Update: We update the ZmDB annotation frequently following the release of a newer GenPept database, or after addition of a large number of new maize ESTs to our database.


Return to Documentation Index | Return to Maize Gene Discovery Project index | Return to Homepage

home  

Be sure to cite us!

This page is HTML 4.01 valid!