[Feedback] Site Feedback: Blast

[feedback at gramene.org]

URL         : http://ensembl.gramene.org/Sorghum_bicolor/Info/Index

Subject     : Site Feedback: Blast

Name        : Hugo Cuevas

Email       : hugo.cuevas at ars.usda.gov

Organization: USDA-ARS

Comments    : 

HI,
I used to use Gramene to do BLAST against Sorghum genome. However, I found that the BLAST search in this new version is not as good as previous version. For instance, I used to do blast for primers (20bp length) and in previous version I had hit, while in this new version don't find hits. However, if I used a longest region which include my primers (the previous 20 bp) it show the expected hit. In other words, don't get hit with short sequences. I am wondering if you can let me know how do blast with small sequences in this new version. 

http://www.warelab.org/bugs/view.php?id=5164