Merge branch 'main' of https://github.com/UPPMAX/UPPMAX-documentation

.wordlist.txt

@@ -2846,3 +2846,46 @@ UniVec
 uppnex
 XFCE
 
+BioProject
+DDBJ
+EMBL
+EPO
+Eukaryotic
+GenBank
+GenPept
+JPO
+LSU
+PIR
+PRJNA
+RefSe
+SSU
+SmartBLAST
+TrEMBL
+Transcriptome
+
+USPTO
+Viroid
+cDNA
+euk
+eukaryote
+eukaryotic
+isoform
+metagenomes
+minimise
+mito
+nucleitide
+pataa
+patnt
+pdbnt
+prok
+prokaryote
+prokaryotes
+rRNA
+ribosomal
+rna
+sptrembl
+subunit
+trembl
+unreviewed
+varsplic
+viroid

docs/databases/blast.md

@@ -30,9 +30,9 @@ Note that:
     When new versions are installed, the directory containing the previous versions is renamed to blast_databases_old
     blast_databases_old is deleted the second data of each month at 00.01
 
-These databases use the "v5" format, which includes rich taxonomic infromation with sequences, and will only work with the Blast tools from the module blast/2.8.0+ and later. Earlier module versions can still be used, but you will need to provide/build your own databases. NCBI no longer updates databases with the older "v4" databases as of February 2020, and they have been deleted from UPPMAX. The final updates of these databases (again, as of this writing nearly two years old) are available from NCBI over FTP at ftp://ftp.ncbi.nlm.nih.gov/blast/db/v4.
+These databases use the "v5" format, which includes rich taxonomic information with sequences, and will only work with the Blast tools from the module blast/2.8.0+ and later. Earlier module versions can still be used, but you will need to provide/build your own databases. NCBI no longer updates databases with the older "v4" databases as of February 2020, and they have been deleted from UPPMAX. The final updates of these databases (again, as of this writing nearly two years old) are available from NCBI over FTP at ftp://ftp.ncbi.nlm.nih.gov/blast/db/v4.
 
-Each NCBI-hosted database also includes a JSON file containing additional medatadata for that particular database. These are found in /sw/data/blast_databases/ and are named databasename*.json. The exact name varies based on the format of the database. For example, the contents of the JSON file for the nr database can be see by running
+Each NCBI-hosted database also includes a JSON file containing additional metadata for that particular database. These are found in /sw/data/blast_databases/ and are named databasename*.json. The exact name varies based on the format of the database. For example, the contents of the JSON file for the nr database can be see by running
 
 cat /sw/data/blast_databases/nr*.json
 
@@ -69,7 +69,7 @@ refseq_select_prot 	protein 	NCBI 	NCBI RefSeq protein sequences from human, mou
 refseq_select_rna 	nucleotide 	NCBI 	NCBI RefSeq transcript sequences from human and mouse, restricted to the RefSeq Select set with one representative transcript per protein-coding gene
 SSU_eukaryote_rRNA 	nucleotide 	NCBI 	Small subunit ribosomal RNA sequences for eukaryotic sequences
 swissprot 	protein 	NCBI 	Swiss-Prot sequence database (last major update)
-tsa_nr 	protein 	NCBI 	Protein sequences from the Trascriptome Shotgun Assembly. Its entries are EXCLUDED from the nr database.
+tsa_nr 	protein 	NCBI 	Protein sequences from the Transcriptome Shotgun Assembly. Its entries are EXCLUDED from the nr database.
 tsa_nt 	nucleotide 	NCBI 	A database with earlier non-project based Transcriptome Shotgun Assembly (TSA) entries. Project-based TSA entries are NOT included. Entries are EXCLUDED from the nt database.
 uniprot_sprot 	protein 	UniProt 	Swiss-Prot high quality manually annotated and non-redundant protein sequence database
 uniprot_trembl 	protein 	UniProt 	TrEMBL high quality but unreviewed protein sequence database