User: toheitka

gravatar for toheitka
toheitka200
Reputation:
200
Status:
Trusted
Location:
Germany/Dresden
Last seen:
1 month, 2 weeks ago
Joined:
3 months, 1 week ago
Email:
t***********@tu-dresden.de

Posts by toheitka

<prev • 15 results • page 1 of 2 • next >
0
votes
2
answers
553
views
2
answers
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 7 weeks ago by toheitka200
1
vote
2
answers
553
views
2
answers
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 7 weeks ago by toheitka200
1
vote
2
answers
553
views
2
answers
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 8 weeks ago by toheitka200
0
votes
2
answers
553
views
2
answers
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 9 weeks ago by toheitka200
1
vote
2
answers
553
views
2
answers
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 9 weeks ago by toheitka200
0
votes
0
answers
372
views
0
answers
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 3 months ago by toheitka200
1
vote
2
answers
223
views
2
answers
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 3 months ago by toheitka200
1
vote
2
answers
223
views
2
answers
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 3 months ago by toheitka200
2
votes
2
answers
223
views
2
answers
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 3 months ago by toheitka200
1
vote
1
answer
198
views
1
answers
Answer: A: Building Hidden Markov Model (HMM) for proteins
... The [HMMER][1] software (which is well documented) can be used to produce HMMs from alignments. As for searching DNA with protein HMMs: * nhmmer can be used to build nHMMs from nucleotide alignments. They can be used to query DNA. * hmmer can be used to build HMMs from amino acid alignments. They ...
written 3 months ago by toheitka200

Latest awards to toheitka

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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1601 users visited in the last hour