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partial sequence matches #1507

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MattyCrowther opened this issue Aug 2, 2022 · 1 comment
Open

partial sequence matches #1507

MattyCrowther opened this issue Aug 2, 2022 · 1 comment

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@MattyCrowther
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When using the sequence match feature, results only appear when there is a 100% sequence match.
So my input looks like this:
https://synbiohub.org/search/sequence=<seq>&
The results only return on 100% match.
For example
https://synbiohub.org/search/globalsequence=atgcagtttaaggtttacacctataaaagagagagccgttatcgtctgtttgtggatgtacagagtgatattattgacacgcccgggcgacggatggtgatccccctggccagtgcacgtctgctgtcagataaagtctcccgtgaactttacccggtggtgcatatcggggatgaaagctggcgcatgatgaccaccgatatggccagtgtgccggtctccgttatcggggaagaagtggctgatctcagccaccgcgaaaatgacatcaaaaacgccattaacctgatgttctggggaatataa&id=1.0&
Returns Matches but:
https://synbiohub.org/search/globalsequence=ttgcagtttaaggtttacacctataaaagagagagccgttatcgtctgtttgtggatgtacagagtgatattattgacacgcccgggcgacggatggtgatccccctggccagtgcacgtctgctgtcagataaagtctcccgtgaactttacccggtggtgcatatcggggatgaaagctggcgcatgatgaccaccgatatggccagtgtgccggtctccgttatcggggaagaagtggctgatctcagccaccgcgaaaatgacatcaaaaacgccattaacctgatgttctggggaatataa&id=1.0&
Will not.
It seems changing the ID value doesn't make a difference.
Is this an incorrect way of using the API, or is it a bug?

@cjmyers
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cjmyers commented Aug 14, 2022

We are doing sequence search using Vsearch (https://vcru.wisc.edu/simonlab/bioinformatics/programs/vsearch/vsearch_manual.pdf). We have also struggled to figure out how to configure it to give "close" but not "exact" results. If you have any suggestions, please let us know.

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