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Old 05-31-2013, 09:30 AM   #1
SDPA_Pet
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Default RDP database

Can I download RDP database from NCBI? There are some database on NCBI ftp (e.g.16SMicrobial.tar.gz, refseq_rna.00.tar.gz). Are these NCBI own database or they are from other sources (just in NCBI format)

I try to download RDP database from here (http://rdp.cme.msu.edu/misc/resources.jsp)

However, after I download it, I am not sure which format (or database) I should use.

I want to use BLASTn to blast my sequences data and my data are not aligned. Should I use Unaligned database from the website?

Also, should I use "Genbank, unaligned". What does Genebank mean on the website? Does it mean RDP_10_32 database in genebank format? or It means the NCBI rRNA database. Can I use it directly for blastn command? or I need to convert the database to NCBI request database.

Best regards,
Ben
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Old 05-31-2013, 11:02 AM   #2
GenoMax
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Default

Quote:
Originally Posted by SDPA_Pet View Post

I try to download RDP database from here (http://rdp.cme.msu.edu/misc/resources.jsp)

However, after I download it, I am not sure which format (or database) I should use.

I want to use BLASTn to blast my sequences data and my data are not aligned. Should I use Unaligned database from the website?

Also, should I use "Genbank, unaligned". What does Genebank mean on the website? Does it mean RDP_10_32 database in genebank format? or It means the NCBI rRNA database. Can I use it directly for blastn command? or I need to convert the database to NCBI request database.

Best regards,
Ben
If you start with the release10_32_unaligned.fa FASTA format file you will have to create a blast database from it. You can't directly use it for blastn. Instructions on how to create a blastable database from a fasta (makeblastdb) file are available at the blast command line help page: http://www.ncbi.nlm.nih.gov/books/NBK1763/

release10_32_unaligned.gb appears to have the same sequences in GenBank format.
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Old 05-31-2013, 12:53 PM   #3
SDPA_Pet
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Originally Posted by GenoMax View Post
If you start with the release10_32_unaligned.fa FASTA format file you will have to create a blast database from it. You can't directly use it for blastn. Instructions on how to create a blastable database from a fasta (makeblastdb) file are available at the blast command line help page: http://www.ncbi.nlm.nih.gov/books/NBK1763/

release10_32_unaligned.gb appears to have the same sequences in GenBank format.
What are those aligned databases for? Are they better for blast?
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