This repository contains a tool to identifiy micropeptides from genome wide multiple species alignments. The micpdp tool 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

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 http://creativecommons.org/licenses/by-nc-sa/4.0/

git clone https://github.com/Drmirdeep/micpdp.git

The tool requires mutliple species alignments for regions of interest to call micropeptides in them. For a whole genome wide analysis maf blocks were downloaded from UCSC and stitched together with the scripts from the stitch_maf package. Detailed instructions on how to build these alignments can be found in the file build_genome_maf_plus_index.txt.

Default scoring of micpdp is done by using Ka-Ks ratios. As an alternative scoring procedure the PhyloCSF tool can be used.

micpdp.pl -m chrI/chrI.maf.stitched.cmpl  -c chrI -l 27 -s species_ce10_reordered -t project_cel -b chrI_refseq.bed -T 0.5 -S  -F stitched_mafs

This will identify micropeptides in transcripts of chromosome I with a minimum length of 9 AA (27 nt => -l 27) and keeps sequences with less than 50% of gaps.