User: adrian.altenhoff
adrian.altenhoff • 650
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Posts by adrian.altenhoff
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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 12 days ago by
adrian.altenhoff • 650
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... 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 9 weeks ago by
adrian.altenhoff • 650
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... 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 12 weeks ago by
adrian.altenhoff • 650
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... 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 3 months ago by
adrian.altenhoff • 650
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... nice to hear it works now. happy computing ;-) Cheers Adrian ...
written 6 months ago by
adrian.altenhoff • 650
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... 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 6 months ago by
adrian.altenhoff • 650
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... Hi Biojl,
I've fixed the problem, please upgrade to pyham >= 1.1.7 e.g.
pip install --upgrade pyham ...
written 13 months ago by
adrian.altenhoff • 650
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... 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 13 months ago by
adrian.altenhoff • 650
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... Maybe important to mention that for this exact application of downloading for one or more whole genomes a fasta file of protein sequences, it is much more efficient to use the download link for all protein sequences in fasta format and filter for the genomes of interest. The URL for the latest versi ...
written 15 months ago by
adrian.altenhoff • 650
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... Dear Sally,
the difference is the expected behaviour. Note that in the Map-SeqNum-ID.txt file, the numeric column (8460 in your example) starts from 1 for every genome. So the 8460 is not a unique ID. The id attribute in the tag of the orthoxml file however must be unique.
About your question to ...
written 15 months ago by
adrian.altenhoff • 650
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Teacher
3 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
15 months ago,
created an answer that has been accepted.
For A: OMA error in stage 2 of 2 stage process
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16 months ago,
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For A: OMA error in stage 2 of 2 stage process
Scholar
2.6 years ago,
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For A: Is this warning fatal in OMA
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For A: Is this warning fatal in OMA
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For A: Is this warning fatal in OMA
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For A: Is this warning fatal in OMA
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For A: Is this warning fatal in OMA
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For A: Is this warning fatal in OMA
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For A: Is this warning fatal in OMA
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For A: Is this warning fatal in OMA
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For A: Is this warning fatal in OMA
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For A: Gene Gain/loss + Duplication Tree
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For A: Gene Gain/loss + Duplication Tree
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For A: What exactly is OMA doing here ?
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For A: Gene Gain/loss + Duplication Tree
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