Questions tagged [bioinformatics]
The science of collecting and analyzing complex biological data such as genetic codes using informatics.
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Pianka’s index on arctic species dietary overlap?
I’m working on a project involving a dietary dataset of three arctic species, and the data was gathered by PCRing plant dna in the stool samples. The data for each plant species is expressed as a ...
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How to get sample details of the MS data files deposited on PRIDE?
I am new to proteomics, and am trying to learn proteomic data analysis. I have a naive question regarding getting the details of each sample associated with the MS data files available through PRIDE. ...
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Are there any fine-scale (< 1 kb resolution) genetic or recombination maps with data released?
For some work I've been doing, I've been spending a lot of time looking for linkage and/or recombination maps that meet these criteria:
Very fine-scale, to the point that the typical resolution or ...
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Should I trim 5'-end of RNA-seq reads?
I want to annotate a genome, I don't have RNA-seq data from the same species but from a sister species, which can be used as evidence for gene prediction/structural annotation.
I trimmed the reads ...
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Unusual Blood Type Inheritance: AB and B = O [duplicate]
My mother has blood type AB-, and my father has B+. It is confirmed that he is 100% my biological father, and my younger brother has B+ blood. However, my blood type is O+. As stated earlier, my ...
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Anyone familiar with studies on computational neuroscience focused on consciousness, particularly in anatomical areas such as ARAS?
I am a first year PhD student in computational biology, interested in diverging my research into computational neuroscience. Currently, I am interested in studies on consciousness in computational ...
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Synthetic biology- how to find right genes for my design?
I have a useful synbio system/design in mind (basically an idea of an engineered microbe which will carry out a specific function). How do I go about finding the right genes/parts/devices for it.
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Bioinformatics Prediction vs. Experimental Results: miRNA Regulation of AMPK/WNT Pathway in High-Glucose Conditions
I am investigating the role of a specific miRNA in high-glucose conditions, particularly its effects on cell proliferation, migration, and metabolism. However, I have encountered a significant ...
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Generating CNVs (DEL/DUP) for exome sequencing data (BAM) and inserting them into BAM
I'm looking at a way of simulating CNVs in exome sequencing data. The CNVs should be random, but cover any region in the exome and there can be several of them per individual. The CNVs must be of ...
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Search for new haplogroups in the full human genome
Have the opportunity to analyze the full genomic human DNA of rare populations. The main hypothesis is that specific haplogroups/haplotypes can be found.
There is very little information about ...
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Should I Use a Dimer or Monomer for Molecular Docking with MaoB?
I am planning to perform molecular docking with MaoB, which is reported in the literature to exist as a dimer. The structure I intend to use is PDB ID 6FW0, which is described as the asymmetric unit ...
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RNA Secondary Structure Prediction Algorithm
I am currently working on my Final Project for the Biomed Datamining class, where the main goal is to 'Predict RNA Secondary Structure'.
I am given a set of RNA sequences in FASTA format and am tasked ...
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Gene sequence retrieval (NCBI gene or ENSEMBLE)
I wanted to retrieve the sequence for MPL gene (exon 10). NCBI gene showed 12 exons for the gene and ENSEMBLE showed only 4 exons. The literature mentions that the pathognomonic mutations in MPL gene (...
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Which is the most accurate protein-protein interaction prediction tool?
Among many tools available for predicting protein-protein interaction, which one is the most accurate? By accurate, I mean most close to experimental data. I shortlisted HADDOCK, ClusPro, GRAMM-X and ...
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How to handle glycan structures for bio-/cheminformatics in Python?
I am currently trying to do some machine learning on biological reaction sequences which include glycans. To represent the substrates and products as vectors I am comparing different fingerprints that ...
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