User: adrian.altenhoff

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700
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Switzerland
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3 weeks, 4 days ago
Joined:
6 years, 9 months ago
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a***************@inf.ethz.ch

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Posts by adrian.altenhoff

<prev • 88 results • page 1 of 9 • next >
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Answer: A: OMA standalone estimating memory use for bacterial genomes
... Hi Andrew, I don't think that the scaling behavior of OmaStandalone is the same for bacterial genomes than for eukaryotes. The formula you use gives a rough idea from a few datapoints and are also rather conservative. The memory consumption depends a lot on the size of the genomes and how related t ...
written 26 days ago by adrian.altenhoff700
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Answer: A: Alignment scores thresholds with DNA
... Hi, when you use OMA standalone with DNA sequences, the program uses an empirical scoring matrix based on DNA sequences. The Smith-Waterman dynamic programming algorithm will compute then the optimal local alignment using a scoring matrix where 50% of the sites are expected to have undergone a mut ...
written 10 weeks ago by adrian.altenhoff700
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Comment: C: oma -c error report
... Hi Sadie, what does it mean that it was running before very well? another version of OMA standalone? or this version on a different machine, or on the login node? Did you install oma or do you just start it from the extracted tarball? what happens if you try to run `python3 -m venv .venv` in the ...
written 3 months ago by adrian.altenhoff700
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Answer: A: can standalone OMA be used on protein fasta (not genome)
... Hi, the aim of OMA is in principle to identify orthologs and paralogs among complete genomes. As a prerequisite OMA computes also Smith-Waterman alignments to identify the homologs in the first place. So in principle you can use OMA to identify the homologous protein pairs. As for the later steps ...
written 4 months ago by adrian.altenhoff700
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Answer: A: Clusters proteins at each taxonomic rank - OMA
... Hi Alejandro, can you elaborate what you're trying to do? I'm one of the OMA developers, but I have a hard time to understand what you're doing. In brief, OMA HOGs are groups of genes that all started diverging from a certain ancestral gene through speciation, so that gives you already gene clus ...
written 5 months ago by adrian.altenhoff700
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Answer: A: Error, 'sequence 1 is too long' OMA Standalone
... Hi Carlos, OMA has a hard limit to only align sequences of less than 100k residues / amino acids. Note that OMA is primarily intended to align protein sequences, coding DNA should work as well, but intron regions are not really supported. I hope this clarifies your question. Best wishes Adrian ...
written 6 months ago by adrian.altenhoff700
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Comment: C: OMA not finding numpy; pip and wget failing
... nice to hear it works now. happy computing ;-) Cheers Adrian ...
written 8 months ago by adrian.altenhoff700
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Comment: C: OMA not finding numpy; pip and wget failing
... Hi, does wget work on your cluster if you run it in the console? often connecting to the outside world requires going via a proxy host on HPC clusters, especially from the compute nodes. if wget works on the login node (try e.g. `wget -O - http://google.com`), I suggest to run the first steps of OMA ...
written 9 months ago by adrian.altenhoff700
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Comment: C: Error in some hog codes using pyham
... Hi Biojl, I've fixed the problem, please upgrade to pyham >= 1.1.7 e.g. pip install --upgrade pyham ...
written 16 months ago by adrian.altenhoff700
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Comment: C: Error in some hog codes using pyham
... Hi Biojl indeed, that seems to be a bug in the pyham library. will fix it asap and release a fixed version on pypi. Thanks for reporting. Adrian ...
written 16 months ago by adrian.altenhoff700

Latest awards to adrian.altenhoff

Scholar 26 days ago, created an answer that has been accepted. For A: OMA error: Writing Part files to general cache area, not a specific dir
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: OMA error: Writing Part files to general cache area, not a specific dir
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: OMA error: Writing Part files to general cache area, not a specific dir
Scholar 18 months ago, created an answer that has been accepted. For A: OMA error in stage 2 of 2 stage process
Scholar 18 months ago, created an answer that has been accepted. For A: OMA error in stage 2 of 2 stage process
Scholar 2.8 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 3.5 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 4.0 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 4.4 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 4.5 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 4.6 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 4.7 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 4.8 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Scholar 4.9 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: What exactly is OMA doing here ?
Scholar 4.9 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree

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