HI Daniele,

I am not sure if I understand you correctly. Are you looking for a DNA alignment tool?

In that case, you can download your genes of interest as FASTA format from the NCBI site and afterwards you can upload them all in the Clustal Omega Multiple Sequence Alignment (http://www.ebi.ac.uk/Tools/msa/clustalo/). Make sure you choose the correct format in this site, namely DNA and not protein or RNA.

If this is what you are looking for and need more assistance, do let me know.

Good luck,

Ali

When searching against the Whole Genome Shotgun Contigs (WGS) and a few of the other genome databases at NCBI, the BLAST tool requires that you enter an organism name to limit the range of the search.  It is usually not productive to search hundreds of mammalian complete genomes when you are using an Escherichia coli query, for example.  You do not need to limit the search to one assembly or one species, you can use the NCBI taxonomy browser to find a reasonable range of organisms to search against, such as all of the gammaproteobacteria WGS genomes (1,122 genomes) if you are interested in them.  Or limit the search more to Enterobacteria (226 genomes in the WGS database) if that is useful.

It can also be highly useful to exclude one or more taxonomic levels.  For example if you know your sequence is Escherichia coli and you want to see how it relates to Salmonella, Shigella and others without parsing past hundreds of Escherichia genomes in the WGS database.

http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=1236&lvl=3&lin=f&keep=1&srchmode=1&unlock

Thanks everyone for your kind answers. I actually need to perform the blast of a sequence on a certain number of genomes (WGS) and I couldn't understand why I wasn't able to create my own database of genomes to work on. Perhaps it's a limitation imposed by NCBI as Artur said, I will take a look at the downloadable software. Thanks!

Daniele