Batch blast - how many sequences possible to enter at one time


I was wondering how many sequences can be blasted at one time using Batch Blast without risking the software to crash. Are there any recommendations?

Many thanks,

We have a 10 Mb restriction for query sequences when you drag and drop a FASTA file. Even though this restriction is not enforced if you paste the sequence(s) in the textarea, 10 Mb is what to keep in mind.

That is several thousand transcripts or proteins. For genome that would be one chromosome or one very large scaffold, or several small scaffolds and contigs.

But then your database size also matters. Like BLASTP-ing just few proteins against the NR database can take a long time to finish and generate very big output. I have seen SequenceServer handle ~ 2 Gb of output just fine on MacBook Pros. You can restrict the number of hits and hsps that are reported, or restrict search by evalue to keep the search results meaningful as well as within computational limits.