User: toheitka

gravatar for toheitka
toheitka230
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230
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Location:
Germany/Dresden
Last seen:
3 months, 1 week ago
Joined:
1 year, 4 months ago
Email:
t***********@tu-dresden.de

Posts by toheitka

<prev • 16 results • page 1 of 2 • next >
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Repetitive DNA: Are representative nHMMs from an Illumina read mapping a good idea?
... Hello Biostars community, I am working with a repeated sequence, representing about 1 % of my genome. I do not have an assembly. I want to generate a nucleotide HMM that works well in detecting my repeat on a wide variety of sequences. Do you have any experience with generating nHMMs directly fro ...
next-gen alignment hmm mapping repetitive dna written 6 months ago by toheitka230
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Comment: C: FlexiDot: highly customizable, ambiguity-aware dotplots
... Hello [a.zielezinski](https://www.biostars.org/u/4700/), we just put forward [FlexiDot v1.04](https://github.com/molbio-dresden/flexidot/tree/master/code) containing your suggested parameter `-M/--mirror`! ...
written 14 months ago by toheitka230
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Answer: A: FlexiDot: highly customizable, ambiguity-aware dotplots
... ##We just released [FlexiDot v1.04](https://github.com/molbio-dresden/flexidot/tree/master/code)! This is a graphic formatting update introducing two parameters, one of them suggested here. Thank you [a.zielezinski](https://www.biostars.org/u/4700/) for your sharing your thoughts! As always, ...
written 14 months ago by toheitka230 • updated 3 months ago by h.mon27k
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Comment: C: FlexiDot: highly customizable, ambiguity-aware dotplots
... Thank you for the suggestion! Some tools as e.g. the EMBOSS polydot package handle plots just like you suggested. (And we even actually plotted like this in very early FlexiDot versions, but then changed this, because most use it the other way round.) I spoke to Kathrin (who is first authoring Flex ...
written 15 months ago by toheitka230
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Comment: C: FlexiDot: highly customizable, ambiguity-aware dotplots
... Thank you a lot for saying this. It makes us happy, since we also love this tool. ...
written 15 months ago by toheitka230
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Answer: A: FlexiDot: highly customizable, ambiguity-aware dotplots
... # New [FlexiDot](https://github.com/molbio-dresden/flexidot) version released: ## Annotation-based shading for all-to-all dotplots! Previously only available for self dotplots, we added **annotation-based shading** to all-to-all dotplots, allowing for new visualizations. As before, annotation infor ...
written 15 months ago by toheitka230
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Comment: C: GCevobase: an evolution-based database for GC content in eukaryotic genomes
... Hello [wangdp123][1], GCevobase looks good. What do the statistics measures "Mean of GC", "Mean of GC1", "Mean of GC2", and "Mean of GC3" mean? [1]: https://www.biostars.org/u/24036/ ...
written 16 months ago by toheitka230
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Comment: C: How to find a specific gene in a assembled genome that is not annotated?
... (and I am biased because I am in love with HMMs...) ...
written 16 months ago by toheitka230
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Comment: C: How to find a specific gene in a assembled genome that is not annotated?
... Yes, [lieven.sterck][1] is right, obviously. I had assumed, [genomax][2] already did that. Upon re-reading, I saw, that probably BLASTn has been used, so I agree, tBLASTn would be the keyword. [1]: https://www.biostars.org/u/23882/ [2]: https://www.biostars.org/u/18713/ ...
written 16 months ago by toheitka230
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Answer: A: How to find a specific gene in a assembled genome that is not annotated?
... It looks to me, as if you should follow this thread "[Building Hidden Markov Model (HMM) for proteins][1]" closely, as both of you want similar things. As for HMMs of your proteins, you could retrieve them using [PFAM][2]. The actin page, for example, is here: https://pfam.xfam.org/family/PF00022 ...
written 16 months ago by toheitka230

Latest awards to toheitka

Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Should I quit PhD program?
Appreciated 16 months ago, created a post with more than 5 votes. For FlexiDot: highly customizable, ambiguity-aware dotplots

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