Vector screening of EST sequence for cotton

Question

[meghasihag]

I am working on analysis of EST sequences for cotton, extracted form dbEST, NCBI. For removal of vector contamination i am using VecScreen. I have subjected approximate 10,000 EST sequences to VecScreen. But every time VecScreen produces same result i.e. "No significant similarity found".

Is It ok.

or i should try any other vector contamination removal tool.

Answer 1

[Prakki Rama]

try to grep a portion of your vector or do a simple BLAT and see, if it is capturing any thing similar to vector. If the hits are spurious you could be sure of no vector in your EST data.