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Here is a shell to run **PLAST**:\\

<code>
#!/bin/bash
#$ -S /bin/bash
. /etc/profile
#$ -o logo
#$ -cwd
#$ -pe threaded 10
cd $PWD
CPUs=10
DB=/db1/nr-nt-fasta-oct-2020/nt
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
</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

Here is a shell example to run **BLAST**:\\

<code>
#!/bin/bash
#$ -S /bin/bash
. /etc/profile
#$ -pe threaded 1
#$ -cwd
source activate blast
export BLASTDB=/db1/nr-nt-oct-2020-v5/
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"
source 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.

**Guide for BLAST usage**

- 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):

<code>
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
</code>

Solve :
This is due to mistakenly use the blast options.

<code>
Error 2:
BLAST Database error: No alias or index file found for protein database [XXX.fa] in search path [/misc/scratch2/XXX:]
</code>

Solve 2:
This is due to mistakenly treat nucleotide database as protein database.

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