Differences

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

--- blast_and_plast [2018/07/04 14:43] – 24.138.71.142
+++ blast_and_plast [2024/11/04 10:14] (current) – 110.239.172.216
@@ Line 1: / Line 1: @@
-Here is a shell to run **plast**:\\
+Here is a shell to run **PLAST**:\\
-#!/bin/bash\\
+<code>
-#$ -S /bin/bash\\
+#!/bin/bash
-. /etc/profile\\
+#$ -S /bin/bash
-#$ -o logo\\
+. /etc/profile
-#$ -cwd\\
+#$ -o logo
-#$ -pe threaded 10\\
+#$ -cwd
-cd $PWD\\
+#$ -pe threaded 10
-CPUs=10\\
+cd $PWD
-DB=database\\
+CPUs=10
-QF=yourquery.fasta\\
+DB=/scratch3/rogerlab_databases/other_dbs/nr_March252023/plast/nr.fasta
-plast -e 1e-10 -max-hit-per-query 1 -outfmt 1 -a $CPUs -p plastn -i $QF -d $DB -o $QF.plout\\
+QF=yourquery.fasta
+plast -e 1e-10 -max-hit-per-query 1 -outfmt 1 -a $CPUs -p plastp -max-database-size 10000000000 -i $QF -d $DB -o $QF.plout -force-query-order 1000
+</code>
+to parse the output see https://perun.biochem.dal.ca/user-wiki/doku.php?id=taxonomy_recovery
-to parse the output see http://129.173.88.134:81/dokuwiki/doku.php?id=dayana_salas_-_utility_scripts_taxonomy_coloring_trees_phylogenetics_mixture_models_domain_architecture_and_more
+Here is a shell example to run **BLAST**:\\
-Here is a shell example to run **blast** using MMETSP database:\\
+<code>
+#!/bin/bash
-#!/bin/bash\\
+#$ -S /bin/bash
-#$ -S /bin/bash\\
+. /etc/profile
-. /etc/profile\\
+#$ -pe threaded 10
-#$ -cwd\\
+#$ -cwd
 source activate blast
-DB=/db1/extra-data-sets/MMETSP/MMETSP_db/MMETSP_DB_clean.v2018.fa\\
+export BLASTDB=/db1/blast-may-2024/
-blastn -db $DB -query yourquery.fasta -out yourqueryresults.blout\\
+DB=nt
-source deactivate\\
+query=your_query.fasta
+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"
+conda deactivate
+</code>
+Both shells use NCBI nt database, but PLAST doesn't support new v5 NCBI nr and nt databases and can cause Segmentation fault error.
+<Last updated by Dandan Zhao on Jun 11, 2024>