User: UBodenhofer

gravatar for UBodenhofer
UBodenhofer230
Reputation:
230
Status:
Trusted
Location:
Johannes Kepler University, Linz, Austria
Website:
http://www.bioinf.jku.at/
Twitter:
u_bode
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Google Scholar Page
Last seen:
3 weeks, 4 days ago
Joined:
5 years, 5 months ago
Email:
b*********@bioinf.jku.at

Associate Professor in Bioinformatics at Johannes Kepler University, Linz, Austria. Maintainer of the following packages: 'msa', 'kebabs', 'procoil', 'podkat' (Bioconductor) / 'apcluster', 'rococo' (CRAN)

Posts by UBodenhofer

<prev • 32 results • page 1 of 4 • next >
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Answer: A: running msa (msa) aborts R session
... In this case, André, I agree that it is a memory issue. If you insist on ClustalW, you may have to resort to the command line version (though I am not convinced that this will work). Maybe you better give ClustalOmega a try, since it is explicitly designed for handling larger data. Sorry that I cann ...
written 5 weeks ago by UBodenhofer230
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Answer: A: Installation of MSA package fails
... I'm glad you fixed it yourself, thanks for letting us know! It seems this was the same issue as described in https://support.bioconductor.org/p/90735/#91679. As an advice to everybody who reads this: if you have an Rprofile.site, check it carefully or install 'msa' in a vanilla R session. ...
written 5 weeks ago by UBodenhofer230
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Answer: A: running msa (msa) aborts R session
... I'm sorry you are encountering difficulties with our package! It is actually quite difficult to guess the source of the problem. Can you provide the sequences for debugging or are they confidential? In any case, there is one thing you can first try yourself: can you use a subset of your sequences an ...
written 5 weeks ago by UBodenhofer230
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Answer: A: msa: How to obtain a subset of an alignment
... Thanks for your positive feedback, Christof!  Regarding your question: yes, it is true that objects of class 'MultipleAlignment' and classes derived from 'MultipleAlignment' do not support subsetting. Presently, I can offer the following workaround (... continuing your example code): alnSubset &l ...
written 3 months ago by UBodenhofer230
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Comment: C: Can't install msa on FreeBSD
... That's why GNU make is listed as system requirement. ;-) ...
written 4 months ago by UBodenhofer230
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Comment: C: Can't install msa on FreeBSD
... Great to know that you managed to solve this issue. I will make some tests to see if your workaround also works on other systems and compilers. If so, I can include it in the release. Note, however, that this code is shipped with ClustalOmega. Can you compile ClustalOmega from source on your system? ...
written 4 months ago by UBodenhofer230
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Comment: C: untranslate AAstringset {Biostrings} or MsaAAMultipleAlignment {msa}
... Please note that more or less exactly the same question has been discussed previously (thread https://support.bioconductor.org/p/96231/). And the answer was the same as by hakunamatata: use DECIPHER. ...
written 5 months ago by UBodenhofer230 • updated 5 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: Using msa msaPrettyPrint(): saving multiple alignement fasta file
... These are not directly related to msaPrettyPrint() or any other 'msa' functionality. Olorin used them for his example posted above. He reads FASTA files from 'workdir' and writes the output of msaPrettyPrint() to 'outdir'. 'bdir' is just the base directory, of which 'workdir' and 'outdir' are sub-di ...
written 7 months ago by UBodenhofer230
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Answer: A: Outputting a multiple alignment to file error: could not find function write.XSt
... The correct name of the function is 'writeXStringSet' (without period). I don't recall precisely when the function name was changed, but I think it was several Bioconductor releases ago. The correct usage is the following: writeXStringSet(unmasked(z), file="test.fasta") The function 'unmasked' ma ...
written 10 months ago by UBodenhofer230
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Comment: C: msaPrettyPrint cannot handle long sequences?
... Of course, that is exactly what I would have answered. If you have any other questions or issues, please let us know. All the best! ...
written 10 months ago by UBodenhofer230

Latest awards to UBodenhofer

Scholar 10 months ago, created an answer that has been accepted. For A: Outputting a multiple alignment to file error: could not find function write.XSt
Autobiographer 19 months ago, has more than 80 characters in the information field of the user's profile.

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