Hello, I am trying to do an ACT comparison using big_blast on two constructions of the same partial genome (one with 4 contigs and one with 3 to see where the various pieces have been joined together). I was therefore expecting large blocks of identical sequence showing rearrangement etc. However, I seem to be getting loads of small blocks. I think that of this is due to multiple repeat elements but I was wondering if it was something to do with the window size used by blastn or the block size by big_blast. Does anyone have any suggestions on how to improve the layout?
Thanks in advance Melanie Duffield Bioinformatics Biomedical Sciences Porton Down Wilts SP4 0JQ Tel (1)980 614364 Fax (1)980 614307 "This e-mail is intended for the recipient only. If you are not the intended recipient you must not use, disclose, distribute, copy, print, or rely upon this e-mail. If an addressing or transmission error has misdirected this e-mail, please notify the author by replying to this e-mail." "Recipients should note that all e-mail traffic on MOD systems is subject to monitoring and auditing."
