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I recently learned about a phenomenon in which asparagine residues can undergo spontaneous intermolecular deamidation reactions to interconvert into a mixture of asparagine, aspartic acid, and isoaspa…
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10/27/21
1. can we use variant-containing sequences as test data?
2. profile vs counts information?
answer: probability output, total counts, if multiple two then come up with per base counts, as…
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Were trying to get an pae_interaction less that 10, but when we put the contig as A100-200/0 70-100 we get i_pae (we assume its the pae_interaction score) as around 26, but when we use contig of 70-10…
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I assume SO_refactored.owl/obo is the output of the compilation step (see #12)
If so, then it differs substantially from the current released version of SO. Some of these are technical and probabl…
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We need a new version of all EMBOSS tools. We should write a converter from [EMBOSS ACD](http://emboss.sourceforge.net/developers/acd/syntax.html) files to Galaxy xml files.
Please get in touch with …
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Terms impacted:
'E-box binding'
'N-box binding'
'RNA polymerase I CORE element sequence-specific DNA binding'
'RNA polymerase I enhancer sequence-specific DNA binding'
'RNA polymerase I upst…
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Hi EVM team,
Thank you very much for this wonderful tool.
I am annotating a plant genome (~500 Mb), that has ~50% repeats that was masked by RepeatMasker. For annotation, I used a soft-masked geno…
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Hi Pete,
I have an interesting case for you. Perhaps an annoying one. I accidentally ran into some variants that suddenly make me doubt the quality of the hg38 mappings using UTA.
When providing…
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Good morning,
I've aligned ATAC-seq data to a five-genomes graph generate through cactus. The alignment was performed through VG 1.23.0, and then I've tried to surject the reads to one of the genomes…
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## The need
Identifying things like RBS motif, start codon, etc. can come in handy with gene-aware analyses. Such analyses may become more frequent in the future especially given the current effort…