ClaireRinehart
Heather,
In the NCBI outputs there are several tagged descriptor lines like: /note and /product. Occasionally, when the editors at NCBI find that a protein has a domain that they feel matches one of the functional domains, they will insert a /region note. Whenever you find a Yes under the Region header in the NCBI BLAST it will be a blue link. If you click on this link a separate window will pop up that will contain the /region note and additional annotation lines from the NCBI output. So, the Region column is just a flag that lets you see that there additional information or confirmation that has been added to the original annotation by NCBI. You will also notice that the Yes / No designators are only present for matches that have greater than a 70% identity, this was an arbitrary cutoff that we chose to save search time.

Enjoy!

Claire

Thanks Claire! That was great. I do have a new question today. In the function window in PECAAN we have no option to choose "integrase" the only options are "serine integrase" or tyrosine integrase". However, there are no instructions that I can find that would give the students a hint about which of these to choose. Does anyone know if this is coming?
The annotated genomes that we are finding matches to all use the function "integrase".

Thanks!
Heather