I am working on a study to detect bacterial and viral particles (organisms) in patient samples. After reading various papers and various posts on this forum; I perform de novo assembly and have contigs. I have read in various papers (e.g http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034631 ; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196430/) that after assembly I have to use tBlastx, they are using the command line version to perform such blast. They also mention that a database for viral genome is created. I found on the web http://nebc.nerc.ac.uk/bioinformatics/docs/tblastx.html but not sure if this is one to follow or i am chasing a wrong target. I would appreciate if some one can direct me to a URL or advice how the database is generated to use tblastx (as mentioned in almost all publications showing detection of pathogen in samples). Is there a work flow which I can follow. Why cannot we use tblastX on NCBI site? How we finally create the database and perform tblastX for such studies.