Scripts to build genome wide alignments and accompanying indices. Package has been used in
Mackowiak at al, Extensive identification and analysis of conserved small ORFs in animals. Genome Biology 2015
Bazzini et al, Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. Embo J. 2014
Gernstein et al, Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 2010
Mangone et al, The landscape of C. elegans 3'UTRs. Science 2010
The scripts, in the form provided in this archive, were implemented by Sebastian Mackowiak, being a PhD student at this time in the lab of Nikolaus Rajewsky at the Max-Delbrueck-Center for Molecular Biology. The code is hereby released under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. You should have received a copy of the license along with this work. If not, see https://creativecommons.org/licenses/by-nc-sa/4.0/
git clone https://github.com/Drmirdeep/stitch_maf.git
For an example use case have a look at build_genome_maf_plus_index.txt and sample_run.sh