BACK
Program: 
Query:  Search query by annotated protein information
Database: 
Uniprot(Swiss-Prot & TrEMBL) plant division contains about 800,000 sequences
Select Rice Annotation data
Please select one of the following database for rice annotation.
RAP IRGSP/RAP build 5 annotation data
MSU Release 6.1

Deselect all - Select all - Collapse all - Expand all -

  • Monocot
    • Oryza sativa (RAP-DB or MSU)
    • Brachypodium distachyon (JGI)
    • Sorghum bicolor (JGI)
    • Zea mays (Maize Genome Sequencing Project)
  • Eudicot
    • Arabidopsis thaliana (TAIR9)
    • Carica papaya (ASGPB)
    • Glycine max (JGI)
    • Medicago truncatula (MGSC)
    • Populus trichocarpa (JGI)
    • Vitis vinifera (IGGP)
    • Fragaria vesca (SGSC)
  • Lycophyte
    • Selaginella moellendorffii (JGI)
  • Moss
    • Physcomitrella patens (JGI)
  • Green alga
    • Chlamydomonas reinhardtii (JGI)
    • Ostreococcus tauri (JGI)
    • Volvox carteri (JGI)
  • Red alga
    • Cyanidioschyzon merolae (Genome Project)
  • Yeast
    • Saccharomyces cerevisiae (SGD)



Detailed options
Maximum number : 
Maximum number of sequences in each species to display
Expect threshold : 
E-value threshold
Filter :  On Off
Mask off segments of the query sequence that have low compositional complexity

Word size : 
Default value is 11 for blastn, and 3 for the other programs.

Mask :  Mask lower case letters
E-value points : 
 Count the number of hits at each E-value

Enter E-value points.(e.g., 1e-10,1e-20).
Multiple number should be separated with a comma(,).

Criterion for   
caluclating MR : 
 Total score (order of priority:1st=Total score, 2nd=E-value)
Max score (order of priority:1st=Max score, 2nd=E-value)
E-value (order of priority:1st=E-value, 2nd=Total score)
Query coverage (order of priority:1st=Query coverage, 2nd=Total score)

  • Total Score: By the sum of scores from all HSPs from the same database sequence
  • Max Score: By the bit score of HSPs, similar to Expect Value
  • E-value: Expect Value
  • Query Coverage: By the percent of length coverge for the query