Mirage
Multiple-sequence IsofoRm Alignment tool Guided by Exon boundaries.
About
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.
Dependencies
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.
Build
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.
Installation
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.