Getting mRNAs coordinates and extracting subalignments

Question

[prosvirov.k]

Hello, dear colleagues,

I need to extract the alignments of 5'UTR from multiple genome alignments in .msa format.My idea is too get the file containing mRNA\CDS coordinates and run through the .msa file and extract subalignments. The,I have a question. How can I get that file with mRNA coordinates in human genome? P.S. If there are any good ideas or other ways of extracting subalignments of 5'UTRs, I`d appreciate them!

Thanks in advance!

Answer 1

[EVR]

Hi,

You can make use of GFF3 or GTF file of the genome to extract the mRNA coordinates. In case if you dont have GFF3 or GTF file for the Genome, you can generate the GFF3 file using PASA or GMAP. In case if you have transcriptome but no GFF3 or GTF file, you can use TransDecoder to generate the GFF3 file your transcriptome.

Key point is generate GFF3 file for your genome or transcriptome which contains coordiantes of mRNA and its CDS location. Later make use of bedtools to extract subalignments.