creating and masking subject database for blast

Question

[kanupriyatiwari4]

Hi,

I have a set of Unigene sequences that I want to align to the hg19 build. I am using blast+ for this purpose and want to create the database using the hg19 chromosomes fasta sequences available at uscs hgdownloads. There are two types of files available i.e. chromFa.tar.gz (which is soft masked acc to their description) and chromFaMasked.tar.gz (which is hard masked). I am confused about which of these files to use for building my subject database for blastn. Can anyone suggest which to use and why? I am new to this topic and appreciate any help.

Thanks!