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 • 193 results • page 1 of 20 • next >
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Comment: C: options for RNA polymerase II-chipseq data using macs2 callpeak
... What did you do in the end? ...
written 4 days ago by Biojl1.6k
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Comment: C: Extract columns from a vcf file using identifiers from a second file
... You are working with MAC right? You have a weird file structure, it has \r (mac) and \n (unix). To fix them you have to remove the \r: [jl@gaia drive-download-20180509T103851Z-001]$ tr -d '\r' < file1.txt > unixfile1.txt [jl@gaia drive-download-20180509T103851Z-001]$ tr -d '\r' < ...
written 12 days ago by Biojl1.6k
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Comment: C: Extract columns from a vcf file using identifiers from a second file
... You should always provide the original files so people can run tests. Also this tr command you are using is removing all tabs preceded by a space... which is not useful at all. If your separating character is one space just try `join -t $' ' <(sort -k1,1 file1) <(sort -k1,1 file2)` ...
written 12 days ago by Biojl1.6k
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Answer: A: Extract columns from a vcf file using identifiers from a second file
... Assuming that the separating character is '\t' I think that join is faster for larger files. In order to use the join command the files have to be sorted by the common field (in this case in both files is the first field, but it could be different). join -t $'\t' <(sort -k1,1 file1) <(sor ...
written 13 days ago by Biojl1.6k
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Answer: A: How to visualize a tree with ancestral state information
... If you want to plot a tree with annotation in an automated way your best bet is ETE: http://etetoolkit.org/ You can do almost anything you want with a tree programmaticly. Is python based. ...
written 4 weeks ago by Biojl1.6k
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Comment: C: How to deal with one-to-many orthologies in PAML
... In general people focus on one-to-one orthologs (and skips one-to-many or many-to-many) in their analyses precisely to avoid this problem. ...
written 4 weeks ago by Biojl1.6k
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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 months 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 months 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 months ago by Biojl1.6k • updated 4 months ago by Pierre Lindenbaum107k
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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 months ago by Biojl1.6k

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Scholar 12 days ago, created an answer that has been accepted. For A: Long Motif Predicted by MEME SUITE
Popular Question 4 months ago, created a question with more than 1,000 views. For convert GFF3 files from one genome version to another (Drosophila)
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Popular Question 8 months ago, created a question with more than 1,000 views. For Obtain conservation (or % ident) in a multiple sequence alignment
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Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Status Quo: Trinity Vs Oases
Scholar 12 months ago, created an answer that has been accepted. For A: Long Motif Predicted by MEME SUITE
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