Differences

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

--- biological-databases [2023/10/05 05:42] – aorth
+++ biological-databases [2026/07/14 06:11] (current) – external edit 127.0.0.1
@@ Line 7: / Line 7: @@
 ^Name        ^Comments   ^Updated¹              ^Database Location          ^
-| nt | NCBI nucleotide collection (v5²) | Dec 21, 2021 | ''/export/data/bio/ncbi/blast/db/v5'' |
+| nt | NCBI nucleotide collection (v5²) | Sep 30, 2023 | ''/export/data/bio/ncbi/blast/db/v5'' |
-| nr | NCBI protein collection (v5²) | Dec 24, 2021 | ''/export/data/bio/ncbi/blast/db/v5'' |
+| nr | NCBI protein collection (v5²) | Sep 30, 2023 | ''/export/data/bio/ncbi/blast/db/v5'' |
 | UniProt's UniProtKB/Swiss-Prot | Manually curated, most reliable | July 1, 2019 | ''/export/data/bio/uniprot/blast/db'' |
 | UniProt's UniProtKB/TrEMBL | Automated curation | ? | ''/export/data/bio/uniprot/blast/db'' |
@@ Line 29: / Line 29: @@
 . Use the following to determine the date of a BLAST database:
-<code>$ module load blast/2.10.0+
+<code>$ module load blast/2.14.1+
-$ blastdbcmd -info -db nt | grep Date
+$ blastdbcmd -info -db nt | grep Date</code>
-</code>
 . In 2019 [[https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/24/have-you-tried-blast-2-9-0-and-version-5-blast-databases-dbv5/|NCBI introduced BLAST database format version 5]] and these only work with BLAST tools starting from 2.9.0. NCBI are no longer updating the version 4 databases, but we have preserved them in a separate directory if you are using tools that do not support version 5:
 ''/export/data/bio/ncbi/blast/db/v4''