User: predeus
predeus • 1.4k
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Posts by predeus
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... If you have a simple text file with your locus tag annotation, you can easily annotate all genes. ...
written 4 months ago by
predeus • 1.4k
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... You can use an online tool like Phantasus: http://genome.ifmo.ru/phantasus-dev/
there are normalization and other options, and you don't need to have any experience in programming. Tutorial is here: http://genome.ifmo.ru/phantasus-dev/phantasus-tutorial.html ...
written 4 months ago by
predeus • 1.4k
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... Thank you.
I've looked at `biomaRt` (and used it quite a few times) before - they seem to have only the most popular microarray platforms (about 30 different ones for human). If you look at GPLs in GEO, there is over 1000 for each human and mouse. Plus there doesn't seem to be an easy way to match ...
written 4 months ago by
predeus • 1.4k
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... There are sometimes "annot" tables, and always the "soft" files. Both contain an annotation table, which varies widely between platforms - very few have actual probe sequences. ...
written 4 months ago by
predeus • 1.4k
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... Hello all,
I was wondering if there is a straightforward way to obtain probe sequences for a microarray platform given the GPL ID. I know that there are varying degrees of annotation for microarrays in GEO - most popular ones have "annot" files, while others have "miniml" and "soft" files. However ...
written 4 months ago by
predeus • 1.4k
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... Thank you for all suggestions - extremely useful! ...
written 6 months ago by
predeus • 1.4k
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... Hello all,
this is a strange question perhaps, but it's brought on by a reviewer to one of my papers. We have used `mafft` to generate multiple sequence alignment for a simple phylogenetic analysis. However, the reviewer suggested we use "method that takes secondary structure of 16S" into account. ...
written 6 months ago by
predeus • 1.4k
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... That's interesting info, thank you. What is the difference in e-value calculation - can you point me to where it's described? Would hit ranking still be preserved? ...
written 6 months ago by
predeus • 1.4k
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... This seems to be a Win 10 - specific bug. I still have Windows 8 and latest blast works fine on my computer, but my wife with Windows 10 couldn't get it to work. Old version did the trick though. ...
written 6 months ago by
predeus • 1.4k
0
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... did blast algorithm change in any substantial way since 2015? I think it was already very, very established by then - so there should be no difference whatsoever in the main components. ...
written 6 months ago by
predeus • 1.4k
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For How To Determine If Library Is Strand-Specific
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For Find All Annotated Rrna (Rdna) Sequences
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17 months ago,
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For Version history and design files for exome kits from Agilent, Roche(Nimblegen), and Illumina
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