blastn for global alignment

Question

[obalasz.spam]

Hello guys,

do you know an approach or settings in blastn, that helps to align more-or-less the full query sequence against a target sequence? I understand that the blast provides local alignments, what I need is a fast, high quality alignment between relatively large genome segments. The emboss needle and some improved versions of it, is just not fast enough.

Thanks,

[GenoMax]

fast, high quality alignment between relatively large genome segments.

Use lastz (LINK). BLAST as the name indicates does local alignments and is not suitable for large genome to genome alignments.