Hi, Is there any function, package that could be used to blastx nucleotide sequences against protein sequences? It should use exclusively the blast program. Thanks, Carol [[alternative HTML version deleted]]

Hello, You could use the function blastSequences in annotate. The BLAST server has a maximum number of queries you can make. If you want your options not to be limited, you can download and install the BLAST programs on your computer, and use them from within R. system("blastn -db nr -query transcripts.fa -evalue 1e-20 -out matched.txt -num_threads 16") You can use this in a Sweave or R markdown document for a completely reproducible analysis. -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia