I am trying to Blast a fasta file of about 5000 sequences. Is there any application, beside Blast2Go, to batch blast? Can the results be saved in a single .xlm file?
What database are you planning to Blast against? 5000 is quite a lot if your going to Blast against something large (bigger than a gb) e.g. the non-redundant database. You might want to run it using a desktop and leave it overnight -> Not on a laptop!
To get XML output, you can command line it by setting: