Albert, you did not mention what speed you intend to achieve. If you only have a couple of sequences, you can just use Smith-Waterman. BWT-SW is also a good choice for mammalian genomes. It has a similar speed to blast for short sequences while gives identical alignment to Smith-Waterman. It is frequently overlooked. BWA-SW can be a reasonable choice when speed is critical. You need to increase "-z" (e.g. 10 or even 100) to achieve high sensitivity. SSAHA2 is also a decent choice. The default setting would not work. You need to ask Zemin about the options.
For mammalian genomes, blast is too slow. Algorithms indexing the genome are usually much faster. I do not know if blast+ gives significant boost. Probably not.
EDIT: People should read the BWT-SW paper [PMID:18227115]. It performs the exact SW algorithm while is faster than blast in the 100-1000bp range. The BWA-SW paper [PMID:20080505] shows that SSAHA2 performs well for 10% divergence. I do not see why it cannot be tuned to work for sequences with the human-mouse divergence. BWA-SW is using the default settings. It may work well with a more sensitive configuration. I am not sure about this bit, though, as I have not tried. Also, modern SSE2/CUDA powered SW is approaching the speed of blast (not yet). PatternHunter is known to work better than blast for cross-species alignment. A few groups (I cannot remember which) have improved blast, though these are less known. A lot happened in the past 10 years in the area of sequence analysis, but blast has not been changed much so far as I know. These efforts are not in vain.
I guess Albert is mapping transcriptome contigs. I think he needs a fast aligner.