Recently I have downloaded the nr database from ncbi website (ftp://ftp.ncbi.nlm.nih.gov/blast/db/). Although, in the readme file it is instructed that the pre-formatted database must be downloaded with update_blastdb.pl script, I downloaded all the 50 files nr.*.gz one by one manually. Can it cause a problem in calculating PSSM matrix using this database?
Secondly, while downloading the database, there was an update in the database files.So some of the files I downloaded are of different updates?As they take a long time, I could not download them all under same update. Will it cause a problem?