Differences

This shows you the differences between two versions of the page.

--- biological-databases [2020/04/08 09:35] – aorth
+++ biological-databases [2020/04/08 09:38] – aorth
@@ Line 8: / Line 8: @@
 ^Name        ^Comments   ^Updated¹              ^Database Location          ^
-| nt | NCBI nucleotide collection (v5) | Mar 24, 2020 | ''/export/data/bio/ncbi/blast/db/v5'' |
+| nt | NCBI nucleotide collection (v5²) | Mar 24, 2020 | ''/export/data/bio/ncbi/blast/db/v5'' |
-| nr | NCBI protein collection (v5) | Mar 24, 2020 | ''/export/data/bio/ncbi/blast/db/v5'' |
+| nr | NCBI protein collection (v5²) | Mar 24, 2020 | ''/export/data/bio/ncbi/blast/db/v5'' |
 | UniProt's UniProtKB/Swiss-Prot | Manually curated, most reliable | 2019-07-01 | ''/export/data/bio/uniprot/blast/db'' |
 | UniProt's UniProtKB/TrEMBL | Automated curation | ? | ''/export/data/bio/uniprot/blast/db'' |
@@ Line 26: / Line 26: @@
 ==== Notes =====
-¹ Use the following to determine the date of a BLAST database:
+  * 1. Use the following to determine the date of a BLAST database:
 <code>$ module load blast/2.10.0+
 $ blastdbcmd -info -db nt | grep Date
 </code>
+  * 2: NCBI introduced database format version 5 in 2019 and these only work with BLAST tools starting from 2.9.0. They are no longer updating the version 4 databses, but we have preserved them in a separate directory if you are using tools that do not support version 5.