User: pixie@bioinfo

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pixie@bioinfo1.3k
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Posts by pixie@bioinfo

<prev • 182 results • page 1 of 19 • next >
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Structure Prediction of Transcription Factor and its binding site to a promoter element
... I have a wild type sequence of a transcription factor. I had predicted its structure using I-Tasser. I have a hunch that the structure might be a tetramer, although here I am getting it as a monomer here. What should I do in this case ? I know the sequence of the promoter element (DNA) to which it ...
structure written 23 hours ago by pixie@bioinfo1.3k
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Answer: A: what next after DEGs?
... Networks may be? Study their interactions/associations , identify hub genes etc. ...
written 1 day ago by pixie@bioinfo1.3k
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Effect of amino acid mutation (deletion) on the protein structure
... I have a wild-type amino acid sequence of a plant. I have a mutated sequence with a single amino acid deletion. I have modeled the protein structure and computed the H-bonds and performed energy minimization using SPDV (swiss PDB viewer). Now, I need to delete a particular residue and perform the sa ...
protein mutation structure written 6 days ago by pixie@bioinfo1.3k • updated 5 days ago by Ram17k
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Comment: C: WGCNA-consensus network analysis using RNA-seq data
... Thanks so much for your time and detailed explanation. I will give a proper thought to this before I jump into network analysis. ...
written 10 days ago by pixie@bioinfo1.3k
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Comment: C: WGCNA-consensus network analysis using RNA-seq data
... Thanks, my only concern was that by merging all the samples of all the conditions in one matrix, am I diluting the any information. But after going through their tutorial, they have possibly done that (i.e. normalized across male and female data) ...
written 10 days ago by pixie@bioinfo1.3k
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WGCNA-consensus network analysis using RNA-seq data
... Hello, I have raw read counts from various stress conditions (4 types) from the same RNA-seq platform and tissue. I had previously determined the DEGs from the individual stresses separately and also extracted their normalized expression matrix for each of the stress conditions . If I wish to perfo ...
rna-seq written 10 days ago by pixie@bioinfo1.3k • updated 10 days ago by andrew.j.skelton735.3k
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Gene regulatory networks from expression data
... Hello, I have RNA-seq data of a plant species. Is it possible to construct a gene-regulatory network, if I provide the transcription factor information ? Most of tools/papers talk about time-series data, but I have static data. I am not interested in co-expression networks. Any leads will be very h ...
network rna-seq written 13 days ago by pixie@bioinfo1.3k • updated 13 days ago by nfs.falsafi20
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Comment: C: Extracting the sequence of isoforms from RNA-seq data
... Thanks Michael, I will check those out! ...
written 5 weeks ago by pixie@bioinfo1.3k
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Extracting the sequence of isoforms from RNA-seq data
... Hello, I have a basic doubt. I have used rMATs to predict alternative splice events in my data. Then I am using IGV to built the sashimi plots to view the junction and exonic reads. Any idea how to extract the sequence for the isoforms ? The organism I am working on has the sequences given only for ...
rna-seq written 5 weeks ago by pixie@bioinfo1.3k • updated 5 weeks ago by michael.ante2.6k
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RNA-seq- Alternative spliceforms
... Hello, I am interested in identifying alternative splice forms from my RNA-seq data ( mutant and wild type samples with 3 replicates each) . We have generated the gene gtf file from ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG3.2_release/ITAG3.2_gene_models.gff Unfortunately, I am unab ...
rna-seq written 8 weeks ago by pixie@bioinfo1.3k

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