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Questions about Blast search command

Hello, I am writing a script for Blast and Pfam search based on this website.

I first check the module on SLURM, it has "Blast-Plus", I am not sure what package is it? can it be used for Blast search?

based on this command 

blastx -query $TRANS_DATA/mouse38_cdna.vol.${SLURM_ARRAY_TASK_ID}.fasta \
    -db $TRINOTATE_HOME/uniprot_sprot.trinotate.pep \
    -num_threads 8 -max_target_seqs 1 \
    -outfmt 6 > blastx.vol.${SLURM_ARRAY_TASK_ID}.outfmt6

I am very confused with the input

$TRINOTATE_HOME/uniprot_sprot.trinotate.pep

is this line supposed to be inserting the location that contains SwissProt within "Trinotate"?

And what makes it difference between BlastX and Blastp ?

Thank you for your time in advance

trinotate
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updated by Asaf Asaf • written by slin023 • slin023

it has "Blast-Plus", I am not sure what package is it?

Current blast search package from NCBI (from v.2.3, as of today v. 2.10.1) is indeed called blast+.

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written by GenoMax GenoMax

1 answer

  1. Yes, this file (should) contain the database of proteins.
  2. blastx takes the DNA sequence, translate in six reading frames and searches the peptides against the database whereas the input for blastp is already peptides.

As a side note, write this as a pipeline in nextflow, snakemake, wdl or any other pipeline management system, it will be much easier to execute. In addition, if you have singularity installed on your system, it's easier to run everything through a container, this way your not bound to the version installed and you can control the version and the environment.

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written by Asaf Asaf

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