Differences

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--- blast_and_plast [2021/09/01 16:35] – 38.20.199.40
+++ blast_and_plast [2024/11/04 10:14] (current) – 110.239.172.216
@@ Line 10: / Line 10: @@
 cd $PWD
 CPUs=10
-DB=/db1/nr-nt-fasta-oct-2020/nt
+DB=/scratch3/rogerlab_databases/other_dbs/nr_March252023/plast/nr.fasta
 QF=yourquery.fasta
-plast -e 1e-10 -max-hit-per-query 1 -outfmt 1 -a $CPUs -p plastn -max-database-size 10000000000 -i $QF -d $DB -o $QF.plout -force-query-order 1000
+plast -e 1e-10 -max-hit-per-query 1 -outfmt 1 -a $CPUs -p plastp -max-database-size 10000000000 -i $QF -d $DB -o $QF.plout -force-query-order 1000
 </code>
-to parse the output see http://129.173.88.134:81/dokuwiki/doku.php?id=dayana_salas_-_utility_scripts_taxonomy_coloring_trees_phylogenetics_mixture_models_domain_architecture_and_more
+to parse the output see https://perun.biochem.dal.ca/user-wiki/doku.php?id=taxonomy_recovery
@@ Line 26: / Line 26: @@
 #$ -S /bin/bash
 . /etc/profile
-#$ -pe threaded 1
+#$ -pe threaded 10
 #$ -cwd
 source activate blast
-export BLASTDB=/db1/nr-nt-oct-2020-v5/
+export BLASTDB=/db1/blast-may-2024/
 DB=nt
 query=your_query.fasta
-blastn -db $DB -query $query -out yourqueryresults.blout -num_threads 1 -outfmt "6 qseqid sseqid evalue pident qcovs length slen qlen qstart qend sstart send stitle"
+blastn -db $DB -query $query -out yourqueryresults.blout -num_threads 10 -outfmt "6 qseqid sseqid evalue pident qcovs length slen qlen qstart qend sstart send stitle"
-source deactivate
+conda deactivate
 </code>
-Both shells using NCBI nt database (/db1/nr-nt-jan-2019/nt.nal), but the formats for specifying DB are different for BLAST and PLAST.
+Both shells use NCBI nt database, but PLAST doesn't support new v5 NCBI nr and nt databases and can cause Segmentation fault error.
-Guide for **BLAST** usage
+<Last updated by Dandan Zhao on Jun 11, 2024>
-blastp:search protein database(e.g., SwissProt db, NCBI-nr) using protein sequence query
-blastn:search nucleotide database(e.g., NCBI-nt, MMETSP_DB_clean.v2018.fa)using nucleotide sequence query
-blastx:search protein database with translated nucleotide sequence query
-tblastn:search translated nucleotide database with protein sequence query
-tblastx:search translated nucleotide database with translated nucleotide sequence query
-Note: blastp and blastx can usually provide better alignments than blastn, especially for distantly related species.This is because amino acids sequences are more conserved than nucleotides (Koonin and Galperin, 2002).
-General bugs when mistakenly use blast options(e.g., blastn or blastp) or query sequence (amino acids or nucleotides sequences):
-Error 1:
-FASTA-Reader: Ignoring invalid residues at position(s): On line 7: 4, 8, 10, 13, 27-29, 32, 42, 45, 51, 53, 56, 63, 66-67, 70, 78
-FASTA-Reader: Ignoring invalid residues at position(s): On line 8: 6, 9, 15, 19-20, 22, 28, 34-39, 45-48, 52
-Solve :
-This is due to mistakenly use the blast options.
-Error 2:
-BLAST Database error: No alias or index file found for protein database [XXX.fa] in search path [/misc/scratch2/XXX:]
-Solve 2:
-This is due to mistakenly treat nucleotide database as protein database.