BLAST database files

Question

[sfcarroll]

After I run makeblastdb against a fasta file, I get nhr, nin, nog, nsd, nsi and nsq files.

Questions

1. What do these file extensions mean?
2. Do these files replace the original chrY.fa file which was indexed, or are they themselves indexes intended to be used in conjunction with the original .fa file?

-rw-rw-r-- 1 sean sean  58M Mar 20  2009 chrY.fa
-rw-rw-r-- 1 sean sean   43 Sep  4 13:32 chrY.fa.nhr
-rw-rw-r-- 1 sean sean   96 Sep  4 13:32 chrY.fa.nin
-rw-rw-r-- 1 sean sean   36 Sep  4 13:32 chrY.fa.nog
-rw-rw-r-- 1 sean sean   18 Sep  4 13:32 chrY.fa.nsd
-rw-rw-r-- 1 sean sean   59 Sep  4 13:32 chrY.fa.nsi
-rw-rw-r-- 1 sean sean  15M Sep  4 13:32 chrY.fa.nsq

Answer 1

[Pierre Lindenbaum]

1. nhr is the header file, nin is the index file, nsq is the sequence file.... But you don't really have to know this. Blast 'just' needs this. They all should be described in the sources.
2. Yes, you can drop the file chrY.fa

[sfcarroll]

Should I give BLAST the chrY.fa.nsq file as the database, or just chrY.fa?

[Prakki Rama]

chrY.fa should be sufficient.

[sfcarroll]

Thanks Prakki

Answer 2

[sfcarroll]

Thank you Pierre for your answer. For anyone interested there is also a good description here, along with a downloadable paper.