Details
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Type:
New Feature
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Status: Closed (View Workflow)
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Priority:
Minor
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 10.0.0 Major Release
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Labels:
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Story Points:3
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Epic Link:
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Sprint:Summer 3 2023 June 12, Summer 4 2023 June 26, Summer 5 2023 July 10
Description
Situation: Under the Advanced Search tab the Search can be set to residues. This is extremely useful as a user can search for primer locations or motifs. While the Residues search does allow for wildcards (.[]*) it does not appear to understand nucleotide symbols such as R [G/A] Y [C/T] etc. So a motif found in a paper such as CACRTS does not work correctly under the Advanced Search for Residues in IGB.
Task: Expand the logic for IGB Advanced Search for Residues so that IGB can understand Nucleotide Symbols.
R A or G
Y C or T
S G or C
W A or T
K G or T
M A or C
B C or G or T
D A or G or T
H A or C or T
V A or C or G
N any base
For example, if a user were to currently use the Advanced Search for Residues in IGB to look for the motif RYSNATCG IGB would not be able to find the motif, as IGB does not understand what RYSN refers to. New logic needs to be added to IGB so that when searching, IGB understands that R can match to either A or G, Y matches C or T, etc.
Attachments
Issue Links
Activity
Pull request submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/932
The PR's source branch is missing a commit that is on the target branch in the target repository - "master".
See: hosted https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/commits/?search=IGBF-3236
To ensure the cleanest possible history, rebase development branch IGBF-3236 onto the most recent commit on the master branch, from the team repository.
To check that my concern is right, run the branch IGBF-3236 installer and look for Kaushik Gopu's name in the credits, as this appears to be the missing commit.
rebased IGBF-3236 onto the most recent commit on the master branch, from the team repo.
pull request submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/933
PR is merged. Master branch installers are built and ready for testing.
Tested on Mac using master branch installer.
Following same testing outlined in previous commit, all searches are working correctly.
Closing ticket.
The CACRTS example is from this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8318262/
The paper is examining the Arabidopsis thaliana genome.