NCBI has an option to 'Align 2 or more sequences' in it's web portal for BLASTP (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&DATABASE=n/a&QUERY=&SUBJECTS=).
As I understand, the main point of doing a local BLASTP is that it allows you to specify a local database - is there any difference between this and putting a load of database sequences in the 'subject sequence' box, when the 'Align 2 or more sequences' option is selected?
I'm assuming making a local DB will result in a faster search due to the database files getting made, and it'll be easier to interact with via code, but I'd be interested to know if there any other fundamental differences.
Maximal number of nucleotides/AA that can be searched via web interface is limited to 1M (nucl) and 100 K (protein) queries. Max number of target sequences is limited to 5K. (LINK).
Great thanks - so essentially seems like a size-limited local blast