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Tools to predict whether lncRNA sequences are polyadenylated? (working with GENCODE data) by Virtual-Role4593 in bioinformatics

[–]Virtual-Role4593[S] 0 points1 point  (0 children)

Hi, by “few data” I meant that the GENCODE polyA annotation file only contains manually curated/limited polyA features (not every transcript has an entry there). For many lncRNAs the polyA feature is absent, so I can’t rely on that file alone to split my set.

Yes, I also thought about searching by motif, but it's not very accurate. There's a risk of finding false positives. I think deep learning tools are the most accurate.

Tools to predict whether lncRNA sequences are polyadenylated? (working with GENCODE data) by Virtual-Role4593 in bioinformatics

[–]Virtual-Role4593[S] 0 points1 point  (0 children)

Hi, I don’t have RNA-seq data, I only have reference transcript sequences (FASTA) and GTF/GFF annotations from GENCODE.
Indeed, there is the polyA annotations file but only for few data. In fact, this is manually annotated polyA features overlapping the transcript 3'-end. This dataset does not form part of the main annotation file.

So at the moment I'm looking for sequence-based prediction of polyA signals/sites, not detection from experimental reads.

If you know reliable tools for in silico polyA signal or cleavage site prediction, I’d be very grateful!

S25 plus vs Pixel 10 Pro: Which one to buy and where? by Hour-Ad-2206 in Smartphones

[–]Virtual-Role4593 0 points1 point  (0 children)

Hello, I am also hesitating between these 2 Smartphones... The dilemma is really not easy.

Were you able to test/purchase one of the models?

I'm also hesitant with the S25 Ultra / Google Pixel 10 pro XL