Dear Yair Cardenas-Conejo,

what kind of sequences do you want to annotate?some specific genes or something else?

i would recomend you to try this tool with BLASTX algorythm :http://www.plantcyc.org/tools/Blast/blast.faces

eventually, it seems logical.

But, if you have sequences, made after cloning, try this tool first, it will allow to detect and delete vector fragments in your files:

http://www.ncbi.nlm.nih.gov/tools/vecscreen/

Dear Anna Solovyeva,

Thanks for you answer.

My sequences are not specific genes, my file contains 52 thousand contigs from a transcriptome and maybe the server not support all the sequences therefore i want to perform all the analysis locally. 

sincerely

Yair