Extracting target from genes using annotation file

[nimarafati]

At the moment, ClustalW is used to do MSA and identify shared regions among all the isoforms. As an alternative we can use a coordinate-based approach to identify overlapping regions among the exons within each gene. To do so we can use the following steps:

• Extracting annotation information of given gene provided by the user from gtf file
• Calculating overlap of the exons
• Choose the regions with highest overlap representing presence of the segment in all the isofrom

[nimarafati]

Based on preliminary result, discussed in a meeting with the research group (@mgcizzu and Mats Nilsson team), we will use consensus and report all the probes by providing scores (showing overlap of the exons or depth; we will check few metrics in the final table).