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🆕 [FEAT] Build custom viral DB #123

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jananiravi opened this issue Feb 5, 2025 · 0 comments
Open

🆕 [FEAT] Build custom viral DB #123

jananiravi opened this issue Feb 5, 2025 · 0 comments
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enhancement New feature or request

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jananiravi commented Feb 5, 2025

Feature: Allow users to select BLAST-searchable databases specialized for viral samples rather than just RefSeq and nr databases.

Biological Question: For people studying viral and especially phage sequences, BLAST default databases like nr do not adequately capture the breadth of viral sequences available especially from metagenomic sources, so queries for viral protein sequences may fall short in addressing research questions in this domain. Can we improve these results by letting people select and search specialized viral databases?

Computational Question: Can we utilize IMG/VR data to expand the pool of homologs we could hit with a viral query? The source database is available for download from JGI, so could we download these data and makeblastDB to turn the IMG/VR database into a BLAST-able option at initial job submission? The browsable database hosted by JGI appears to have accession IDs in the form of UViG ID values which may permit link-outs, and lineages are also called in these data. How much of these data could be integrated into the results with a custom database like this?

@jananiravi jananiravi added the enhancement New feature or request label Feb 5, 2025
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