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User: Biojl

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Biojl • 1.5k
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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 • 179 results • page 1 of 18 • next >
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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 6 days ago by Biojl • 1.5k
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Comment: C: What is the difference between counts and expression level?
... https://www.biostars.org/p/124826/ ...
written 10 days ago by Biojl • 1.5k
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Answer: A: DESeq2 + de novo assembly
... If you use kallisto you should use Sleuth, which is the DE tool designed for that kind of quantification. Also is easier to use than DESeq2. I would focus on the fraction of transcripts with a blast hit, unless you have very good evidence that there are a number of genes that are not conserved beyo ...
written 4 weeks ago by Biojl • 1.5k
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Answer: A: Software for Tree Visualization
... My favourite is [ETE3][1]. You can draw beautiful trees, personalize them to an unprecedented level but most importantly, it allows you to programatically work with trees, asking all sort of questions and even storing information you generate within the trees. A true jewel for researchers working w ...
written 4 weeks ago by Biojl • 1.5k
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Mobile elements studied in the 1000 genomes
... Hi, I am trying to download the set of transposable elements for which frequencies were estimated in phase 3. The publication is this one: http://www.nature.com/nature/journal/v526/n7571/full/nature15394.html However, when I download the supplementary material (Table_4_MEIs.xlsx, sheet G) I can s ...
transposable elements 1000 genomes data written 4 weeks ago by Biojl • 1.5k
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Answer: A: Long Motif Predicted by MEME SUITE
... What are your input sequences for MEME? ChIP-seq peaks for a particular transcription (which one?) factor perhaps? Which is the species you are working with? Motifs coming from transcription factors are typically 4 to 30 base pairs long, but longer motifs have been described in particular cases. ...
written 8 weeks ago by Biojl • 1.5k
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Comment: C: how to get a list of genes affected by a transcription factor?
... Check ENCODE: https://www.encodeproject.org/ ...
written 8 weeks ago by Biojl • 1.5k
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Comment: C: how to get a list of genes affected by a transcription factor?
... In which species are your working? ...
written 8 weeks ago by Biojl • 1.5k
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Comment: C: compare peaks in a gene list (coordinates)
... cat "file a" | wc -l cat "file b" | wc -l Those commands will give you the number of lines which in a bed file will be the number of peaks. If you want to do more in depth comparisons I recommend you use bedtools or the pybedtools library for python. ...
written 11 weeks ago by Biojl • 1.5k
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Comment: C: compare peaks in a gene list (coordinates)
... I do not fully understand your question, can you refine it or give an example? Perhaps a simple "join" command will do what you want ...
written 11 weeks ago by Biojl • 1.5k

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Commentator 10 days ago, created a comment with at least 3 up-votes. For C: Biostar Ads Are Here! Showcase Your Accomplishments To The World!
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Status Quo: Trinity Vs Oases
Scholar 8 weeks ago, created an answer that has been accepted. For A: Long Motif Predicted by MEME SUITE
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Obtain conservation (or % ident) in a multiple sequence alignment
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Calculate Pairwise Wilcox.Test For Several Categories And Plot Significance Into A Boxplot With Ggplot2
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