User: The

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The160
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Posts by The

<prev • 53 results • page 1 of 6 • next >
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Answer: A: Extracting important gene with similar expression level from multiple samples
... How about selecting genes with least variance across samples? Otherwise some clustering will give you genes with similar expressions ...
written 6 hours ago by The160
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Answer: A: Secondary Structure Alignment Method
... If I correctly remember , there was a paper in PNAS by George D Rose in late 90s which dealt with this. The goal was to find out structurally similar sequences based on predicted secondary structure. So far I remember they employed a simple scoring system (match/mismatch binary type): ![enter imag ...
written 17 hours ago by The160
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Comment: C: How to "linearize" or "unfold" a PDB format structure to secondary structure?
... yes, as Michael wants to preserve the well defined secondary structure elements ...
written 2 days ago by The160
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Answer: A: How to "linearize" or "unfold" a PDB format structure to secondary structure?
... Can this help, with default values? I guess it outputs the model in PDB format as well "We set the default for the backbone dihedral angles to the extended conformation (ϕ = −120∘, ψ = 140∘, ω = 180∘)." [PeptideBuilder: A simple Python library to generate model peptides][1] [Github repository][2] ...
written 2 days ago by The160
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Comment: C: Convert a two-column file to a single file with interlayed rows
... No problem for Notepad++, you can convert EOLs to unix style '\n' to windows '\r\n' and vice versa, under the EDIT-> EOL Conversion menu ...
written 7 days ago by The160
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Answer: A: Convert a two-column file to a single file with interlayed rows
... For this type of simple conversion , I would use regex based find-and-replace features of text editors like Notepad++, provided the file is not too big for the editor to open . ![Notepad++ Regex][1] [1]: https://i.ibb.co/0V3VpyT/fasta-Convert.png ...
written 7 days ago by The160
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Answer: A: Get identical elements and index from 2 Arrays in Perl
... use strict; use warnings; my @A = ("Red", "Green", "Yellow"); my @B = ("Yellow", "Black","Yellow","Red", "White", "Yellow"); foreach my $col (@A){ my @hit_indices = map{$B[$_] eq $col ? $_: () }(0..$#B); scalar(@hit_indices) ? print $col, " at indices ",join(',',@hit ...
written 7 days ago by The160
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Forum: Good books on application of Machine Learning in Bioinformatics
... Hello all, I'm looking for books on applications of machine learning and statistical data mining in bioinformatics with example codes provided in R and/or python. I came across the following two books: the first being a quite good one, provides the code in MATLAB, which i'm not very comfortable wi ...
bioinformatics forum book machine learning written 8 days ago by The160
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Answer: A: Good questions and answers resources (forums) on Ecology and Statistics
... http://www.talkstats.com/ ...
written 8 days ago by The160
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Comment: C: how to calculate the log2 median-centered intensity in onconmine
... Try the Iglewicz and Hoaglin formula: y.z <- 0.6745 * (y-median(y,na.rm=TRUE))/mad(y) https://www.itl.nist.gov/div898/handbook/eda/section3/eda35h.htm ...
written 20 days ago by The160

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Popular Question 3 months ago, created a question with more than 1,000 views. For Distance between two gene sets
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Scholar 4.4 years ago, created an answer that has been accepted. For A: Mapping multiple expression data on KEGG genes and metabolites

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