Details
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Type:
New Feature
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Status: Closed
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Priority:
Major
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Resolution: Fixed
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Affects Version/s: None
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Fix Version/s: 2.11.4.0
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Component/s: None
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Labels:None
Description
Dear Jalview developers,
I have been working with Kay Diederichs as an end user to develop a clustering technique for sequences - PaSiMap. It is unique in that it separates sequences by random and systematic features http://pasimap.biologie.uni-konstanz.de/home - I have found it quite useful for assessing titin domain relationships (https://doi.org/10.1016/j.csbj.2022.09.034). It has managed to produce meaningful groups and identity new repeats that were not possible to do with other clustering techniques such as CLANS or PCA.
Although what it is doing under the hood is different, it gives a similar output to PCA. I see that Jalview has a PCA calculation and output function. Would it be possible to integrate PaSiMap calculations into Jalview in the same manner? Although we have a website I think inclusion into Jalview would greatly increase its reach and useability.
Best Wishes,
Jen
I have been working with Kay Diederichs as an end user to develop a clustering technique for sequences - PaSiMap. It is unique in that it separates sequences by random and systematic features http://pasimap.biologie.uni-konstanz.de/home - I have found it quite useful for assessing titin domain relationships (https://doi.org/10.1016/j.csbj.2022.09.034). It has managed to produce meaningful groups and identity new repeats that were not possible to do with other clustering techniques such as CLANS or PCA.
Although what it is doing under the hood is different, it gives a similar output to PCA. I see that Jalview has a PCA calculation and output function. Would it be possible to integrate PaSiMap calculations into Jalview in the same manner? Although we have a website I think inclusion into Jalview would greatly increase its reach and useability.
Best Wishes,
Jen