User: Joel Wallenius

Reputation:
10
Status:
New User
Location:
Sweden
Last seen:
13 hours ago
Joined:
7 months ago
Email:
j************@gmail.com

MSc in Bioinformatics at Lund University.

Primarily interested in solving the aging problem. Eternal youth for everybody woop woop!

Background in astrophysics. I would rather program than think about study designs.

Posts by Joel Wallenius

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Given a list of RefSeq homo sapiens mRNA transcripts, what is the simplest way t
... Sadly I can't rely on the protein alignments though I know they are better suited for homology in most cases. I must go by the transcripts since what I'm interested in is the exact conservation of a base-pair sequence motif. I'm starting to suspect that I shouldn't worry too much about finding the ...
written 10 days ago by Joel Wallenius10
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Comment: C: Given a list of RefSeq homo sapiens mRNA transcripts, what is the simplest way t
... I am completely unfamiliar with these programs. Like you say it seems very complicated. I was thinking that a question such as mine would have been asked many times before. Why would the answer be so complex, then? :/ ...
written 10 days ago by Joel Wallenius10
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Given a list of RefSeq homo sapiens mRNA transcripts, what is the simplest way to get the corresponding sequences from some other related species?
... Hello! I have a list of RefSeq accession numbers of mRNA transcripts, all from homo sapiens, and would like to, for each transcript, get the corresponding transcript (and its sequence) from a number of related species like mouse rat cow monkey etc. I can't imagine that there isn't already a databa ...
alignment orthology transcriptome written 13 days ago by Joel Wallenius10
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Interpreting the output of an mRNA structural motif search algorithm
... Hello! I am searching for motifs in some hundreds of mRNA sequences. I couldn't find any, so now I'm searching for structural motifs instead. I am not familiar with any such software so I just used the first one that worked without hassle - 'RNAProfile'. Its output includes some patterns like (((. ...
mrna motif structure written 12 weeks ago by Joel Wallenius10 • updated 12 weeks ago by Martombo2.0k
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Comment: C: Given a protein domain, like a TPR or zinc finger or some other one, can you pre
... That is remarkably close though. I tested it, it couldn't find any significant matches. Perhaps TPR regions are way too diverse for such a tool... ...
written 3 months ago by Joel Wallenius10
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Given a protein domain, like a TPR or zinc finger or some other one, can you predict what RNA sequence it binds to?
... Hello! Question in the title. I am trying to find out if there is a tool somewhere that takes a protein sequence or structure and predicts what RNA sequence it binds to. This is about finding out if there are stretches of RNA in some mRNA transcripts that bind to particular transport proteins and ...
rbp rna affinity protein written 3 months ago by Joel Wallenius10
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Comment: C: Getting MPI to work with MEME suite CPU parallelization in OpenSuse
... Alright. I finally got it working by downloading openmpi from the developer's website, installing it in my home folder, and specifying that installation folder while configuring MEME. I will never trust YaST again when it comes to niche or avant-garde software :( Thank you regardless, Alex! ...
written 3 months ago by Joel Wallenius10
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Comment: C: Getting MPI to work with MEME suite CPU parallelization in OpenSuse
... How customized is it? Could it still be used for standard motif discovery? ...
written 3 months ago by Joel Wallenius10
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Comment: C: Getting MPI to work with MEME suite CPU parallelization in OpenSuse
... Ah, I understand now. Why do you have such a makefile? I received help from the OpenSUSE irc chat, apparently meme couldn't on its own find the mpicc/mpirun installation directory. So weird... but it works now. Thanks a huge bunch though! ...
written 3 months ago by Joel Wallenius10
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Comment: C: Getting MPI to work with MEME suite CPU parallelization in OpenSuse
... The MEME readme says to install by: 1. configure --prefix=$HOME/meme --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt 2. make 3. make test 4. make install Are all of those four steps replaced by the steps that you described? If yes, do I only replace the standard ...
written 4 months ago by Joel Wallenius10

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