User: Biojl

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Biojl1.7k
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Posts by Biojl

<prev • 201 results • page 1 of 21 • next >
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Comment: C: Error in some hog codes using pyham
... I am able to generate the pyham_analysis object but one of the things I want to do is generate a TreeProfile for a specific HOG as explained here. https://zoo.cs.ucl.ac.uk/tutorials/tutorial_pyHam_get_started.html#genomedef It requires hog_of_interest = ham_analysis.get_hog_by_id(HOG_ID), there is ...
written 4 months ago by Biojl1.7k
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Error in some hog codes using pyham
... Hi, I am having trobules with the pyham library to access OMA database from python. #Python3 from omadb import Client c = Client() prot_id = 'PADI1_HUMAN' r = c.proteins[prot_id] # Can also be called as c.proteins.info(prot_id) import pyham # Initialise pyHam ...
oma written 4 months ago by Biojl1.7k • updated 4 months ago by clement.train10
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Comment: C: Download cdna sequences from OMA
... Thanks you very much! ...
written 11 months ago by Biojl1.7k
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Comment: C: Download cdna sequences from OMA
... There is not. I don't want to download a 2.4Gb compressed file and parse it every time I want the cDNA of a bunch of orthologs. There is an option to download all the ortholog protein sequences when you search a particular protein. I was looking for the same with cDNA. ...
written 11 months ago by Biojl1.7k
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Comment: C: Download cdna sequences from OMA
... Yes, this is what I did, but it would be nice to have a bulk download of cDNA for selected sequences, just as there is for proteins ...
written 11 months ago by Biojl1.7k
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Download cdna sequences from OMA
... Hi, I am trying to obtain the cdna sequences for orthologs groups. There is a button for *Download: Fasta* but apparently it only works for the protein sequences. Does anybody know if there is a way to download them in bulk as opposed to download every single sequence individually? ...
orthologs oma written 11 months ago by Biojl1.7k • updated 11 months ago by adrian.altenhoff620
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Comment: C: calculating dn/ds from codeml output
... Are your running codeml through biopython? Is relatively easy to parse the output: https://github.com/biopython/biopython/blob/master/Bio/Phylo/PAML/codeml.py ...
written 16 months ago by Biojl1.7k
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Answer: A: Find transcription factors that may regulate list of genes
... What about calculating a Log odds ratio (LOR) using a pre-defined area around your genes of interest. Count the number of TFBS in those regions and compare it against the whole genome and/or other genes not related to the modules you want to test, to correct for the effect of having genes around you ...
written 16 months ago by Biojl1.7k
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Comment: C: options for RNA polymerase II-chipseq data using macs2 callpeak
... What did you do in the end? ...
written 17 months ago by Biojl1.7k
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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 17 months ago by Biojl1.7k

Latest awards to Biojl

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?
Great Question 7 months ago, created a question with more than 5,000 views. For Where To Get A Mammalian Phylogenetic Tree With Branch Distances.
Appreciated 8 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?
Popular Question 11 months ago, created a question with more than 1,000 views. For Where to obtain a gene rpkm matrix for mouse (from mouse encode)
Great Question 14 months ago, created a question with more than 5,000 views. For Where To Get A Mammalian Phylogenetic Tree With Branch Distances.
Scholar 17 months ago, created an answer that has been accepted. For A: Long Motif Predicted by MEME SUITE
Popular Question 21 months ago, created a question with more than 1,000 views. For convert GFF3 files from one genome version to another (Drosophila)
Popular Question 21 months ago, created a question with more than 1,000 views. For Where to obtain a gene rpkm matrix for mouse (from mouse encode)
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Where to obtain a gene rpkm matrix for mouse (from mouse encode)
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Where to obtain a gene rpkm matrix for mouse (from mouse encode)
Popular Question 2.1 years 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 2.4 years ago, created an answer with at least 3 up-votes. For A: Status Quo: Trinity Vs Oases
Scholar 2.5 years ago, created an answer that has been accepted. For A: Long Motif Predicted by MEME SUITE
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Obtain conservation (or % ident) in a multiple sequence alignment
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Status Quo: Trinity Vs Oases
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Automatic Data Extraction From Timetree
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Biopython And Codeml Module. Error.
Popular Question 3.7 years ago, created a question with more than 1,000 views. For How To Parallelize Codeml With Python
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