Sequence alignment viewer for a custom database
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2.7 years ago
pixie@bioinfo ★ 1.4k

Hello, I have developed a pilot database for SNP data for various genotypes in my plant specie. I have used Python-Flask framework with Sqlite3 as the back-end. I have the sequence data for all the genes for every genotype.

I want to have a feature such that if a user wants to view a given gene for multiple genotypes, the server can display the multiple sequence alignment across the selected genotypes. Is there any plugin/program available for this ?

Thank You

sequence-alignment MSA database clustal • 587 views
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Hi, are you looking for a specific platform/programming language? If Java is an option for you, the GC4S library (http://www.sing-group.org/gc4s/) has a easy-to-use component called MultipleSequenceAlignmentViewerPanel which can be used to display aligned sequences. You can see it in action here: https://github.com/sing-group/GC4S/tree/master/gc4s-multiple-sequence-alignment-viewer

Regards.

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Thanks Hugo for the lead, I will look into it

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