User: toheitka

gravatar for toheitka
toheitka160
Reputation:
160
Status:
Trusted
Location:
Germany/Dresden
Last seen:
1 day, 11 hours ago
Joined:
1 week, 6 days ago
Email:
t***********@tu-dresden.de

Posts by toheitka

<prev • 10 results • page 1 of 1 • next >
0
votes
0
answers
287
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 10 days ago by toheitka160
1
vote
2
answers
131
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 10 days ago by toheitka160
1
vote
2
answers
131
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 10 days ago by toheitka160
2
votes
2
answers
131
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 10 days ago by toheitka160
1
vote
1
answer
106
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 10 days ago by toheitka160
4
votes
5
answers
471
views
5
answers
Comment: C: Should I quit PhD program?
... I don't know about the situation in the US, but over here, informatics/statistics PhD students are more difficult to attract for a biology lab. If one of our students told me, he/she wanted to pursue an integrated biology/informatics project, the lab would profit much: If the student is able to anal ...
written 10 days ago by toheitka160
1
vote
2
answers
108
views
2
answers
Answer: A: Determining ploidy from fungal genomes
... You might try to analyze the **kmer distribution** from your reads. For this, you might use - KmerGenie: http://kmergenie.bx.psu.edu/ , or - Jellyfish: http://www.cbcb.umd.edu/software/jellyfish/ and count your kmers for a few different kmer lengths, e.g. 17mers as in the example. Then, you would ...
written 13 days ago by toheitka160
6
votes
0
answers
288
views
0
answers
Tool: FlexiDot: highly customizable, ambiguity-aware dotplots
... ##We just released the first public version of [FlexiDot][1]: FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for st ...
dotplot visualization tool sequence analysis written 13 days ago by toheitka160
0
votes
3
answers
1.1k
views
3
answers
Answer: A: dotplot with python
... ...so it has been 17 months... but maybe you are or someone stumbling across this thread is still interested in Python dotplotting. ##FlexiDot: We implemented **FlexiDot** in Python, which is a relative feature-rich dotplot suite, covering many issues you might encounter, if you like dotplots. We t ...
written 13 days ago by toheitka160
0
votes
9
answers
9.8k
views
9
answers
Answer: A: Is There Any Stand Alone Dot Plot Program?
... Maybe you'll enjoy **FlexiDot**: It is well documented, implemented in Python and controlled with the commandline. It allows all-against-all, pairwise and self dotplots, and comes with many features, such as - Combination of structural annotations (gff3) with dotplots, or - LCS similarity shadin ...
written 13 days ago by toheitka160

Latest awards to toheitka

Commentator 10 days ago, created a comment with at least 3 up-votes. For C: Should I quit PhD program?
Appreciated 11 days 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: 641 users visited in the last hour