User: adrian.altenhoff

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420
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Switzerland
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2 weeks, 5 days ago
Joined:
4 years, 10 months ago
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a***************@inf.ethz.ch

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Posts by adrian.altenhoff

<prev • 55 results • page 1 of 6 • next >
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Answer: A: Download cdna sequences from OMA
... Dear Biojl, currently there is no way to directly get the cds sequences from all the proteins in an OMA group or HOG from the web interface. However, there is a way how you can get them with quite little programmatic effort from the REST API. Here's a possible way how you could get them in python a ...
written 19 days ago by adrian.altenhoff420
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Comment: C: OMA Standalone: "could not read the right number of characters"
... Hi djw, no idea, kirill.grigorev did not get back to me - so I assume it was this problem. if for you this is not the case would you mind sharing the dataset (or parts where the error happens) with me? you can reach my by email on contact at omabrowser org. ...
written 24 days ago by adrian.altenhoff420
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Comment: C: OMA standalone:"Error, (in ReadFastaWithNames) length(seqs) = length(refs), asse
... sounds to me like it could be an issue with the newline format. is the data on a shared windows folder? you could try to run [dos2unix][1] on these fasta files. To rule out some issues with Bio-linux (I've never used it), you could also try to export a small dataset from the [omabrowser][2] and chec ...
written 7 weeks ago by adrian.altenhoff420
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Comment: C: OMA Standalone: "could not read the right number of characters"
... It looks like the fasta file of DB/homo_sapiens.fa is corrupted. Does it contain any non-unicode characters or ascii char 0 in it? you can also send me this fasta file if you are unsure how to check. the email adresse would be contact at omabrowser.org. ...
written 11 weeks ago by adrian.altenhoff420
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Comment: C: OMA Standalone: "could not read the right number of characters"
... Hi, this is likely related to some softlinks in input data or cached databases. could you retry to rerun with -d 10 and let us know about the error. thanks! Adrian ...
written 3 months ago by adrian.altenhoff420
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Comment: C: Trying to hack OMA to do specific All-v-All searches
... Hi Jason, you could simply have a wrapper shell script that assigns the environment variables THIS_PROC_NR=$Process + 1 and NR_PROCESS=100: #!/bin/bash export NR_PROCESSES=100 export THIS_PROC_NR=$(($Process+1) oma you would then submit this wrapper script. This would be a simple ...
written 4 months ago by adrian.altenhoff420
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Answer: A: OMA standalone error
... Hi @pbravakos currently Esprit works only on protein sequences, or in principle coding DNA (but parameters certainly have not been optimised for that). The error you get indicates that you probably are using also intronic gene sequences or even entire contigs. ...
written 4 months ago by adrian.altenhoff420
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Answer: A: Error, (in OrthologousMatrix) values cannot be ordered
... By commenting out the `InparalogTol` and `ParalogTol` parameters the two variables are undefined and numeric comparisons of expressions involving these two variables are no longer possible. You need to assign values to them, this should fix your problem. ...
written 7 months ago by adrian.altenhoff420
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Answer: A: OMA output does not match settings
... In OMA we integrate data from many different sources. So it's quite difficult to have a coherent, comprehensive set of cross-references. Because of this we add our internal OMA-IDs, which are the UniProt species codes + a number and fall back to those in case we cannot identify one of the canonical ...
written 7 months ago by adrian.altenhoff420
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Comment: C: how to resume an oma job using grid engine
... What do you mean exactly with resume? did you stop the process? or did oma terminate? in that case, you can simply resubmit it - it will continue from where it left off. ...
written 7 months ago by adrian.altenhoff420

Latest awards to adrian.altenhoff

Scholar 11 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 20 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 2.2 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 2.5 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 2.6 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 2.7 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 2.8 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 2.9 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Scholar 3.0 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: What exactly is OMA doing here ?
Scholar 3.0 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree

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