User: mschmid

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mschmid90
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Switzerland
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http://thvd.net/
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2 weeks, 4 days ago
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5 years, 2 months ago
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Posts by mschmid

<prev • 80 results • page 1 of 8 • next >
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Answer: A: ClustalO computing suboptimal alignment
... I tried MUSCLE and it seems to do a much better job. ...
written 4 weeks ago by mschmid90
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Comment: C: ClustalO computing suboptimal alignment
... Yes, MUSCLE seems to do a much better job for my application. Strange though.... ...
written 4 weeks ago by mschmid90
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ClustalO computing suboptimal alignment
... Clustal Omega - 1.2.4 I align about 600 (n) highly identical sequences. n-1 sequences are identical. There is one sequence which has some differences. For some regions I get an alignment which is obviously suboptiomal (gap is one base to early). EDIT: This is just one example. Obviously I could ju ...
alignment clustalomega written 4 weeks ago by mschmid90
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Answer: A: Where to find a list of (sequenced) WHO reference strains
... My problem is to identify/find those assemblies. Fetching them from NCBI Assemblies database is no problem. Do they have a special tag? How do I identify them? And I am still interested in a database with all WHO reference strains. ...
written 5 weeks ago by mschmid90
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Where to find a list of (sequenced) WHO reference strains
... The world health organisation (WHO) is defining WHO reference strains for some pathogens (Need it mainly for bacteria and virus). And I guess many of them are sequenced. Does anyone know where to find this database and where to fetch the corresponding genome assemblies? ...
genome written 5 weeks ago by mschmid90
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What does 1V1 exactly mean?
... In the context of sequence alignment: What does 1V1 exactly mean? For example mentioned in this recent preprint (Pages 2 & 4): https://www.biorxiv.org/content/biorxiv/early/2019/02/26/546630.full.pdf ---------- **Edit:** As genomax pointed out this seems to describe the similarity of the s ...
alignment polishing written 9 weeks ago by mschmid90 • updated 9 weeks ago by ATpoint16k
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JGI databases vs GenBank
... I am really confused about this Do the JGI databases contain genome assemblies which are NOT deposited on NCBI GenBank? If yes, how can I retrieve them? Both systems seem really redundant to me doing their own thing for the same purpose. So basically I want to fetch all bacterial genome assemblie ...
ncbi jgi img written 10 weeks ago by mschmid90 • updated 10 weeks ago by Juke-342.2k
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Comment: C: Majority of genes upregulated in RNA-seq study of toxic compound
... Yes, sure, sequencing deeper would be the easier method ...
written 5 months ago by mschmid90
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Comment: C: Majority of genes upregulated in RNA-seq study of toxic compound
... Hmm... OK. Like this it makes sense. That would mean Ideally one has a bit more Replicates for the control to counter for this effects? ...
written 5 months ago by mschmid90
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Comment: C: Majority of genes upregulated in RNA-seq study of toxic compound
... OK, added some more info. Hope it gets clear now. ...
written 5 months ago by mschmid90

Latest awards to mschmid

Scholar 4 weeks ago, created an answer that has been accepted. For A: ClustalO computing suboptimal alignment
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Correct substitution model for yeast - RAxML
Popular Question 5 months ago, created a question with more than 1,000 views. For Correct substitution model for yeast - RAxML
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Popular Question 5 months ago, created a question with more than 1,000 views. For SMRT analysis- what is difference between RS_HGAP_Assembly.2 vs RS_HGAP_Assembly.3
Supporter 5 months ago, voted at least 25 times.
Great Question 14 months ago, created a question with more than 5,000 views. For MiSeq: R1 vs. R2 reads show big quality difference - is that normal?
Popular Question 14 months ago, created a question with more than 1,000 views. For How to find pseudogenes in bacteria
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