Add additional trailing amino acids for frameshift insertions when creating fasta #1155
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
When we create the fasta file for making binding predictions, we only include n-1 flanking amino acids so that each n-length substring of the peptide overlaps the mutation position. However, for inframe insertions that duplicate of a longer region, the insertion position (insertion start) is not where the mutated amino acids start (which is at the end of the duplicated region). Currently, not enough flanking amino acids are included in the fasta file pVACseq creates. This PR extends the end of the MT and WT peptide sequences for inframe insertions by the length of the insertion on top of the specified flanking region. This ensures that the duplicated portion of the WT sequence is always fully included.
Closes #1152