[Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database
Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Fri Jun 5 19:16:59 CEST 2020
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From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Paul Shannon <paul.thurmond.shannon using gmail.com>
Sent: Friday, June 5, 2020 1:12 PM
To: Nystrom, Spencer <snystrom using email.unc.edu>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database
Thanks, Spencer. Sorry I missed the support posting - there�s no automatic forwarding from there to maintainers.
I�ll take a look at this later today, then post back to the support list, and we will get a fix in.
Thank you for pointing out the problem!
> On Jun 5, 2020, at 9:46 AM, Nystrom, Spencer <snystrom using email.unc.edu> wrote:
> I've identified a few missing PWMs from the MotifDb package and would like to help get them added. I posted on the support page but have not received a response after 10 days, so messaging here instead (link to forum post: https://secure-web.cisco.com/1TFAehHIfvF8C-fsHqKF9EZUlEaLQqYsIygNO_BAsoXZwv_Wu3u5B4wJVetP6b2oLhIIOFSZhhOumdKzED0ovgHBPNyPVtPXiHxRm8b66_DTxd3gOar2MNQ5l9qQH4_wqJMMJaxbnBCWUwAGnSDJO91ueABvVc6mU2FAghpGjUfBlWvlYMMhZzzmbgjYqsldl1Ta23cGowoJ3ncf7CeSKr6bKFMch5qHT0BqRq0t6Gi_b7w1KzlscAc0wC3Pxjq5gXX9vMchpSqTrtO3_MRw3Ojfo2wOimSuSsQL0RWe2mKIGnuSE0r8q7XSF0fsyFaH-DmeMbMdAxJok14mifZioaA/https%3A%2F%2Fsupport.bioconductor.org%2Fp%2F131312%2F). Full details can be found in the support post, but in summary, there are a small number of Drosophila transcription factors which do not have any entries in MotifDb, meaning anyone using that database for their motif analysis will not identify these factors as potential candidates. A .meme format file ("flyFactor_Missing_Motifdb.meme") of these missing motifs along with a reproducible script to identify these factors can be found at this gist: https://secure-web.cisco.com/1Hw4j-u2eWVf5hZXzqLZ4apPGgjUddOX5ixtNdTGwQZ4NPy_KaMZids5AaShi-S2meTRVKS9jM3cf2iEulIctx81-ZyEXDGgnDv79mSzGZG0QjWEwCoKwaCa8Eg2m1zL4AW14psIhbcmvxc36OZX77cPdvVBZBl0WIzqa0g6N2n6c75iPRS0Mi4k86awArVwZ6SMWbd9onXyqHQqqfNpEcQnilZw0UkOntlEVSBQWpNszEdDH6zw1gLuglq1F4JIJwa6onOYuveddTXIVT0r3veLCqhDXiDZIxFN9PmMrUUh9Xqiq2S2uRkK53JqfA-krBLQfCwo4agchyGpfqwWZOA/https%3A%2F%2Fgist.github.com%2Fsnystrom%2Fb7701858bec6bc4ce7758a7582422359. I am happy to help curate any additional metadata required to get these factors added to the database.
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