BLAST chapter -query in param summary

[oneilsh]

from first ed:

"...
-query
The name (or path) of the FASTA-formatted file to search for as query sequences.
-subject
The name (or path) of the FASTA-formatted file to search in as subject sequences.
-evalue
Only HSPs with E values smaller than this should be reported. For example: -evalue 0.001 or -evalue 1e-6.
..."

missing in current ed :)

[petersm3]

FYI

Not suggesting this should be included in the book, but I always cited it in the Canvas discussion forums when teaching BLAST:

Nidhi Shah, Michael G Nute, Tandy Warnow, Mihai Pop, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, Bioinformatics, Volume 35, Issue 9, May 2019, Pages 1613–1614, https://doi.org/10.1093/bioinformatics/bty833

"The BLAST (Altschul et al., 1990) alignment tool has been the workhorse of genomics research for almost 30 years. While many other tools were developed during this period for performing database searches and sequence alignment, BLAST remains the tool of choice for many use cases, and continues to be actively used in many bioinformatics workflows. Despite the tremendous collective experience of the bioinformatics community with BLAST, the full functionality of this tool remains poorly understood. Here we report on a feature of BLAST that operates in a non-intuitive way and that is frequently misused in bioinformatics workflows, potentially leading to erroneous results impacting numerous scientific articles."

Also related: https://blastedbio.blogspot.com/2015/12/blast-max-target-sequences-bug.html