Koeng101 / Koeng101/dnadesign

Megamash cannot call complicated sequences

Open
#64 10 comments 0 reactions 0 assignees View on GitHub
enhancement
Dominant language
Go
Stars
38
Forks
1
PR merge metrics
No merged PRs in 30d

Description

`seq_recovery=0.4152_0` for example, cannot be processed into a megamash table because it doesn't have any unique 16mers. This is because of a flawed assumption: ESPECIALLY in protein variant libraries, 16mer windows won't necessarily be unique - and even if a sequence is unique, a 16mer sliding window may not be able to pick it up. This is a real issue.

I'm still trying to figure out how to fix this.

[templateMap.csv](https://github.com/Koeng101/dnadesign/files/14300542/templateMap.csv)

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reproducing the megamash failure with seq_recovery=0.4152_0 and inspect the attached templateMap.csv. Trace how sequences are converted into a megamash table and identify where the unique-16mer assumption rejects this input. Done means complicated protein variant sequences can be processed without requiring unique 16mers.

Written by the indexing model from the issue text.

Assessment

Tech stack
go
Domain
bioinformatics
Issue type
Bug
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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