synbiohub icon indicating copy to clipboard operation
synbiohub copied to clipboard

partial sequence matches

Open MattyCrowther opened this issue 2 years ago • 1 comments

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?

MattyCrowther avatar Aug 02 '22 14:08 MattyCrowther

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.

cjmyers avatar Aug 14 '22 22:08 cjmyers