Hi, Ariel! Thanks for the pointer to the big_blast.pl script.
I got it to work on my computer. The script chops up the query into pieces of a size that I can define in the script and blasts each piece against the database. This is better than before but I am getting the "Reached max 200> HSPs in BlastSaveCurrentHsp, continuing with this limit" error for every single piece, although I went down to a piece size of 50bp. Since blast stops after 200 HSPs and just cuts off the rest, the result are not useful. Certain regions would falsely appear as having no homologue region in the query genome. The solution to this would be to divide the database into smaller pieces as well, blast every piece of the query against every piece of the database and assembling this again, thus resulting in a quadratic algorithm. Anyone doing a tblastx of two genomes must have run into this problem. What did you do about it? Greetings from Germany, Michael. ----- Original Message ----- One way is to use the bigblast.pl script. There was a link to the script in the Artemis page, or try googling. Best regards Ariel Amadio _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
