User: Biojl

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Biojl1.6k
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Biologist

Protein ALignment Optimiser (PALO) is an algorithm for the selection of the best combination of protein isoforms among orthologous genes in the construction of a multiple alignment. You can easily upload your files from ENSEMBL and this tool will tell you which is the most suitable combination for you to align. http://evolutionarygenomics.imim.es/josepl/codeigniter/index.php/pages/view/home http://gbe.oxfordjournals.org/content/5/2/457

Posts by Biojl

<prev • 187 results • page 1 of 19 • next >
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Comment: C: parse xml proteinpredict files
... Wow, definitely is worth it to learn how to use XSL!! Just one question about the code, in which part you select the info for the first column (ADRB2_HUMAN)? I don't understand this language yet. ...
written 4 weeks ago by Biojl1.6k
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Comment: C: parse xml proteinpredict files
... Is not there, is a made up protein ID. The protein ID is usually in the file name. ...
written 4 weeks ago by Biojl1.6k
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Comment: C: parse xml proteinpredict files
... I'm interested in the info inside this feature: ... Some example lines inside those tags: The idea would be to get: ENSP0001, helix, 89, 108 \n ENSP0001, strand, 109, 113 ...
written 4 weeks ago by Biojl1.6k • updated 4 weeks ago by Pierre Lindenbaum104k
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Comment: C: parse proteinpredict files
... Hi, I have updated the question with the relevant information, including an example file. I am not familiar with XSL stylesheets but I'll dig into it. ...
written 4 weeks ago by Biojl1.6k
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parse xml proteinpredict files
... Hi, I have several thousands of xml files from https://www.predictprotein.org/ calculations for different proteins. I was wondering if anyone knows a package to parse that information in python or R in order to be able to perform some calculations easily. I am mostly interested in the secondary st ...
proteinpredict parse biopython xml written 4 weeks ago by Biojl1.6k • updated 4 weeks ago by Pierre Lindenbaum104k
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Comment: C: how to plot unique genes for 103 samples
... Perhaps you are looking for a venn diagram... Are you interested in the number of genes that are unique to each sample? ...
written 8 weeks ago by Biojl1.6k
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Comment: C: kallisto + sleuth: no results
... Can you paste the full code? ...
written 6 months ago by Biojl1.6k
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bulk download in ENCODE
... Hi, I'm trying to download several experiments in bulk from https://www.encodeproject.org/. I use the filters in the experiment matrix and I come up with 97 datasets. I am only interested in bed narrowPeak files (in available data), thus I select only that category. But when I click download I get ...
encode chip-seq download written 7 months ago by Biojl1.6k • updated 7 months ago by Ming Tang2.2k
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Answer: A: Extract motif ids of all transcription factors in human
... You can programatically access the JASPAR 2016 database using this R package: https://bioconductor.org/packages/release/data/experiment/html/JASPAR2016.html ...
written 8 months ago by Biojl1.6k
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Comment: C: What is the difference between counts and expression level?
... https://www.biostars.org/p/124826/ ...
written 8 months ago by Biojl1.6k

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