blast - difference between database and subject

Question

[hpatzenhauerova]

Hi, I am beginner in this area and I am not able to resolve the option -subject in blast. It seems that it represents sequences which are compared to query sequences, but how it differs from database then?

[GenoMax]

Are you referring to the -subject option for blasting 2 sequences together? In that situation you are not using a database.

[hpatzenhauerova]

yes, I do not understand when you need to use it

[GenoMax]

You would use it when you are trying to blast two sequences together. One file will contain your query sequence and other will contain the sequence you are searching against. e.g. blastn -task blastn -query query.fa -subject sub.fa -out blast_out.txt

[agolicz]

If I remember correctly there is a difference in e-value depending on whether you use -db or -subject.

[Lucila]

Hi genomax, a bit late to this post but I am interested in it. When I do my blast searches, I usually use the -db option where I put the path to a multifasta file that contains, for example, a transcriptome I am searching in (previously formatted with formatdb) . As -query, I put the path to a multifasta file with a list of sequences I am interested to find in the transcriptome. So the question is: is this ok? what if I use -subject instead of -db? Thank you!

Answer 1

[Sej Modha]

https://www.ncbi.nlm.nih.gov/books/NBK1734/

BLAST is an acronym for Basic Local Alignment Search Tool and refers to a suite of programs used to generate alignments between a nucleotide or protein sequence, referred to as a “query” and nucleotide or protein sequences within a database, referred to as “subject” sequences.