Do you have any suggestiong for mapping cDNA reads using Lastz?

I imagine the gaps caused by splicing cause problems for mapping cDNA reads using the commonly used setting?

You're correct here.

Maybe setting up a "cDNA" mapping setting would be helpful, if such a thing is possible with LastZ.

I looked through the LastZ documentation but didn't see anything that would support mapping cDNA to a reference genome.

I suppose an alternative would be to map with bowtie, trimming all the reads to be equal length?

You could try this, but splicing is likely to prevent good mapping. A better alternative is to use Tophat: http://tophat.cbcb.umd.edu/ Tophat is a splice junction mapper; Tophat, among other outputs, provides a list of mapped reads in SAM format. We have a very simple version of Tophat running on our test server that you try out: http://test.g2.bx.psu.edu/ We'll have a more complete version of Tophat up in the next day or two.

A caveat: Tophat is designed for Illumina data, so you may not get optimal results when using 454 data.