swScore of Repeat elements
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Filipe Gracio
Nov 19, 2014, 10:59:51 AM11/19/14
to gen...@soe.ucsc.edu
Hi Good afternoon,
I have a query about the swScore in repeat elements table. I'm not sure I understand what it's computed against. Between the element in that row (with a particular genomic coordinate etc) and what? Thank you very much!
Filipe
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Dr Filipe Gracio
Senior Bioinformatician
(KCL Honorary Research Associate in the School of Medicine)
NIHR Biomedical Research Centre - Translational Bioinformatics Core
Matthew Speir
Nov 25, 2014, 4:30:46 PM11/25/14
to Filipe Gracio, gen...@soe.ucsc.edu
Hi Filipe,
Thank you for your question about the swScore column in the RepeatMasker table. The swScore is the the Smith-Waterman alignment score between the repeat element template sequence, from the RepBase library, and the genomic sequence. For more information on RepeatMasker and its output, see the following help page: http://www.repeatmasker.org/webrepeatmaskerhelp.html#reading. For more information on the RepBase Library, see the following page: http://www.girinst.org/repbase/update/index.html.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
Thank you for your question about the swScore column in the RepeatMasker table. The swScore is the the Smith-Waterman alignment score between the repeat element template sequence, from the RepBase library, and the genomic sequence. For more information on RepeatMasker and its output, see the following help page: http://www.repeatmasker.org/webrepeatmaskerhelp.html#reading. For more information on the RepBase Library, see the following page: http://www.girinst.org/repbase/update/index.html.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
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