I would like to have suggestions into how I could solve this problem:

I have downloaded several cDNA from Ensembl, such as: ENSG00000139618. I have aligned them with other proteins, trimmed unnecesary bits and deleted some regions. Then, I run these alignments in some other program and I get a list of interesting aminoacid positions. The problem is, that I would like to map these positions (based on the trimmed alignment) to the equivalent original protein sequence, from where I got my initial sequences (ENST00000380152.7).

I am not too sure how to approach this. I was thinking of aligning my trimmed, translated ENSG00000139618 with the reference where I want my final positions (ENST00000380152.7). However, I do not know any software that would return my positions based on the reference.

Here I will try to show an example:

>Trimmed_sequence
-----M**P**RAFAAA-A-**R**TA--GH  
  #interesting positions are P 7 and R 17

>Ensembl_original_sequence
M**P**RAFADDDDAAA**R**TAGH 
   #interesting positions are located elsewhere and I would like those positions, which are now: P2, R14

It is not only deleting the gaps in the trimmed alignment, because there might be also insertions in the original sequence that were trimmed.

I would be grateful for any thoughts you might have on this.