User: Anand Rao

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Anand Rao210
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210
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United States
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10 hours ago
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7 years, 10 months ago
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a*********@gmail.com

Posts by Anand Rao

<prev • 138 results • page 1 of 14 • next >
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Comment: C: HHpred installation problem
... Did you figure where to download the following files: pdb70.**a3m**.tar.gz, and pdb70.**hhm**.tar.gz I'm encountering the same issue as you did, with little support from soeding Lab GitHub (most people involved in this have graduated and busy with their current jobs) Any help would be deeply appr ...
written 10 days ago by Anand Rao210
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Comment: C: Using row order of one heatmap for a new heatmap
... Thanks for your suggestion, Ram. I am installing ComplexHeatmap and its dependencies currently. Looks like ComplexHeatmap output be converted to a grob, based on a post [here][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/110 ...
written 15 days ago by Anand Rao210
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Using row order of one heatmap for a new heatmap
... I've generated a heatmap from my 1st input file containing a ( 315 row * 48 column ) grid of 0s and 1s, plus column and row names - please see after downloading [file1][1]) I need to use order of row names from this x, y clustered heatmap to constrain how I make my next plots, which need to be: ...
R heatmap row reorder plot written 15 days ago by Anand Rao210
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Comment: C: How can I perform pairwise comparison of protein secondary structure?
... Thanks for sharing your idea. I've used hhblits in the past, so even though it is computationally more intensive, use of the CS219 alphabet and higher sensitivity of HHM<=>HHM alignment should offer enough info in the output to answer my question. Speaking of output, from the HHsuite HHM-HHM ...
written 18 days ago by Anand Rao210
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Comment: C: How can I perform pairwise comparison of protein secondary structure?
... Thanks for suggesting SSEA, I could not find it elsewhere. I've pinged Silvio Tosatto, hope to hear back from him... ...
written 18 days ago by Anand Rao210
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How can I perform pairwise comparison of protein secondary structure?
... Greetings! Is it possible to perform **pairwise comparison of protein Secondary Structure** where: 1st primary protein sequence = '**Unknown** domain' or 'Uncertain annotation' (~ 20K of these, all different)) 2nd primary protein sequence = **Known** protein domain sequence (~ 500 of these, also ...
secondary structure structure alignment protein written 18 days ago by Anand Rao210 • updated 18 days ago by Mensur Dlakic210
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Comment: C: HISAT2 V.S. STAR
... - Based on their latest respective releases, do you still consider STAR better than HISAT2? - What are the qualifications behind this assertion, are they different from before? ...
written 21 days ago by Anand Rao210
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Comment: C: HISAT2 V.S. STAR
... - Based on their latest respective releases, do you still consider STAR better than HISAT2? - What are the qualifications behind this assertion, are they different from before? ...
written 21 days ago by Anand Rao210
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Evaluating protein structure predictions
... I am new to protein structure prediction. A protein structure informatics expert at my institution advised me to first check quality of structure predictions, before any downstream use. My 2-step pipeline is: Step 1. Structure prediction with LOMETS or I-TASSER Step 2. Structure evaluation with Pro ...
protein structure evaluation proq qmean written 22 days ago by Anand Rao210 • updated 19 days ago by jgreener70
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Comment: C: Protein structure to classify domain sequences into full Vs. partial lengths and
... Thanks for your response. I'll reiterate what I want to do in very simplistic language - "find out if and how prediction of structure for a protein domain can verify if its sequence is really the domain that HMMER3 says it is" One suggestion was to use hhblits to identify best aligned PDB chain to ...
written 25 days ago by Anand Rao210

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Popular Question 29 days ago, created a question with more than 1,000 views. For Feeding FASTA-ggsearch36 results for MCL clustering
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