Getting complete genome in BLASTn

[elflira]

When I use BLASTn to search for alignments, I get some alignments as well as some information about their location in the genome. I was wondering whether there is anyway to get the entire genome of each "hit", since I would like to gather information about the regions before the alignment.

Many thanks,
AG

[rhinoceros]

Sure, as long as the subject genome has been sequenced you can for example download it from the ncbi ftp.

[mikep]

Assuming you used the legacy blastall package and used formatdb with -o to create the index files, you can retrieve the sequence with fastacmd, If you used blast+ then it's makebalstdb and blastdbcmd