Multiple-sequence IsofoRm Alignment tool Guided by Exon boundaries.

Mirage produces multiple sequence alignments of proteoforms by mapping sequences back to their constitutive exons on the genome and then reducing those mappings to alignments that preserve the proteoforms' exonic structures.

Mirage has no build dependencies beyond the C standard library, but it does have several runtime dependencies. These are described below. Executables should exist somewhere in the user's PATH.

blat - http://www.kentinformatics.com/index.html

hsi - https://github.com/TravisWheelerLab/hsi

spaln2 - http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/

tblastn - https://blast.ncbi.nlm.nih.gov/Blast.cgi

Appropriate versions of these are included in the dependencies directory of the repository. The SETUP.pl script will build and install them.

Building Mirage requires a modern C compiler. Use the CC environment variable to control the compiler used. Set the WORK_DIR environment variable to control where the binaries end up, the default is dist.

Then, building is as simple as running make.

Once the build is complete, run make install to copy binaries. Use the PREFIX environment variable to control the install location. The default location is /usr/local.