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A feedback loop is a network structure in which the gene is able to regulate itself via a single path. $A\rightarrow B\rightarrow C\rightarrow A$ Interactions can be called positive or negative depending on their effect on the downstream gene. If a gene A represses another gene B, then it is a negative interaction; when it activates then the interaction is ...


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I know this question is going to close. But, if you want to work something you can work on: Cryo super-resolution fluorescence imaging Highlights CryoFM allows imaging of vitrified biological samples with fluorescence microscopy. There are significant challenges to achieve high-resolution cryoFM imaging. Fluorophore characteristics at low ...


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Actually the new data set will be, for k = 4 (k-mer value) CGTTCT -> CGTT GTTC TTCT or Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874646/


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Options: You can always download the data (as @WYSIWYG has suggested in the comment). Transfer the data to Galaxy Convert and export the selection of your choice. Source: http://modencode.oicr.on.ca/fgb2/gbrowse/fly/


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You can try the R package dendextend. The function tanglegram can do the trick. Several associated functions are also available for getting plots with minimum entanglements such as untangle_step_rotate_2side.


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As per your requirements I will suggest: http://www.onezoom.org/


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Positive and negative feedback are essential motifs that control transcriptional activity of genes. They may involve other genes, mRNA and/or proteins. A classical pattern of negative feedback is where transcription of a gene results in mRNA and translation of this mRNA in a protein that represses the expression of the gene again. Feedback loops may involve ...


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When you say RPKM do you mean crude RPKM or the estimates that you get using expectation maximization methods like cufflinks and eXpress? It is better if you get your RPKM or FPKM values from one of these programs because you can differentiate between transcript variants. I have mostly used cufflinks and eXpress. Cufflinks package is better for multiple ...


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I don't know what a "typical" biologist is, but I'd guess they don't know much about computers, because the population in general is computer illiterate. In my department, we do have a lab that does a lot of computational work on proteins. And of course bioinformatics relies on computers. I can see where programming would come in handy for an ecologist, ...


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With awk it is as simple as this (Assuming that the sequences are in fasta format and the sequences are not interrupted by line breaks): awk -v p=<some_patttern> '/>/{name=$0} !/>/{ s=$0 while (match(s,p)){ print name,substr(s, RSTART, RLENGTH) s=substr(s, RSTART+RLENGTH) } }' fastafile.fa This script will print all ...


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I'm no expert in MATLAB but I know that it is possible to do regular expressions in MATLAB with the general rules explained here. However there are alternative approaches and softwares you could use to achieve this with softwares that are freely available and quite powerful in performing such functions. Although I'm aware that perl and python are the ...


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Use BioMart. It retrieves UniProt information and you can select the features that you want. These files wont be that huge. So you can download it in your PC and SFTP to wherever you are doing your analysis. A better way is to install BioMart in your workstation. See the BioMart documentation.


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Getting SNP data from FTP Site of NCBI SNP: It's actually simple to download the data from the NCBI, if you follow the method given by FAQ( as given by @WYSIWYG). Step 1: Goto organism FTP: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ Step 2 Open your required organism folder: From here you can download any file you wanted. If you trying to study ...


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I don't know what background you have given the kids or what level, but here's something we do in a non-majors freshman level biology course that could easily be adjusted. First, to get them thinking about trees and relationships, give them a simple family genealogy (use only 1 parent for simplicity). I use my family tree going back to my grandmother. With ...


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I would suggest the course of Coursera.org: Computational Molecular Evolution By Anders Gorm Pedersen Technical University of Denmark (DTU) PS: Do tell us if you found a better book!



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