Help on getting multiple alignment for PhyloCSF

[xiaolichen0]

Hello Dr. Lin,

Thanks a lot for the contribution of PhyloCSF. I'm trying to use PhyloCSF to evaluate the likelihood that some novo ORFs were protein coding. These ORFs were found by performing ORF-RATER on our Ribo-seq data. I'm trying to feed the multiple alignments of these ORFs to PhyloCSF.

To make these multiple alignments, I downloaded the mm10 Multiz Align (Multiz60way) table (maf format) from the UCSC table browser. When I tried to extract the multiple alignment of these new ORFs, most of them were "NNNNN...". It seems the mm10 Multiz Align table doesn't contain the regions of these ORFs. I was wondering if you have a more comprehensive maf or have a better way to get the multiple alignment given the regions of interest in mouse genome. Any help will be appreciated. Thank you in advance.

Best Regards,
Xiaoli