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10

You can validate the interactions by knockding down (KD) or overexpressing (OE) a gene and checking the change in expression levels of the downstream nodes. You can do this in a high throughput fashion using microarray or RNAseq. For protein you can do an LC-MS. However this method cannot help you in: Differentiating direct vs indirect interactions Finding ...


6

fastq-dump can write to stdout ; the -Z option allows you to do that. This, you can pipe to any downstream process. [An example]. Also see the SRA-toolkit manual. I guess someone asked this question in biostar too.


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ImageJ is a multi platform piece of software that has a cell counter module that might be of some use, and hey its free! Its easy to use and so ludicrously crude that it is very versatile. I remember using it in undergrad to count cells under the microscope automatically after a few image contrast tweaks. I don't see why this couldn't be reapplied to count ...


2

You can start with deterministic model using ODEs for reaction rates. However, if you are considering diffusion then you would have to use Partial differential equations for Fick's diffusion law. You can, however, assume that there is no "diffusion" but just transport of the signal molecule from a well mixed system (medium) to another well mixed system ...


2

As WYSIWYG pointed out, fastq-dump can output to STDOUT, so if you want to combine it with named pipes, you'd do: mkfifo mydata.fifo fastq-dump -Z mydata.sra > mydata.fifo & cat mydata.fifo # or whatever rm mydata.fifo If you try to catch the output from fastq-dump without -Z it fails with the Illegal seek(29) error: mkfifo mydata.fastq fastq-dump ...


2

It is a common practice to prove a result using an orthogonal technique. Like RNAseq followed by qRT-PCR etc. Western blotting is not a robust technique and cross comparisons are difficult because of difference in the avidities/affinities of different antibodies. So comparisons can be made only with one protein-control pair in different conditions. LC-MS ...


1

Huameng Li and Chenglong Li have done multiple ligand docking in two (AFAIK) of their works: Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of protein Drug Design Targeting Protein–Protein Interactions (PPIs) Using Multiple Ligand Simultaneous Docking (MLSD)..... The method is called Multiple Ligand Simultaneous ...


1

STRING does not distinguish between different products of the same gene. E.g. for human, the protein identifier you see (ENSP...) corresponds to the longest splice form for each gene (ENSG...). Therefore, STRING won't help you if you need to distinguish between splice forms. Splice forms are merged because for most sources of evidence, there is little data ...


1

Okay, so just for others who might stumble upon this, here is a brief description of one implementation of this technique to run with paired-end RNA-seq data: fastq-dump SRA_file --split-files -I -Z | tee >(grep '@.*\.1\s' -A3 --no-group-separator > namedPipe_1) >(grep '@.*\.2\s' -A3 --no-group-separator > namedPipe_2) >/dev/null This first ...


1

The number of hydrogen bonds cannot actually be said from software only inferred. But you could try using STRIDE (http://structure.usc.edu/stride/) which takes the file name with a -h flag to output the number of hydrogen bonds. You could then write a small shell script which would pass in each file and store the data you wanted in whatever format you liked. ...


1

The basic problem is one of prior knowledge. The information you have about E. coli metabolism is in the form of a simple network, i.e. a list of nodes and the edges (along with their weights) that connect them. From this information alone it's impossible to know, for example, that the reactions in the TCA cycle should be plotted as a perfect circle (that's ...


1

I'm not sure if they will be useful for your application, but you should look into software used to visualize ecological networks (and maybe also software used for drawing electrical charts). The type of data used there is very similar to what you want to plot, with nodes and links along with metadata for links on e.g. rates or connection strenghts. I can ...


1

If the gene is supposed to be well conserved then you can use the sequence from the related species. For protein coding genes target the ISH probe to the coding region which is more likely to be conserved. What you can also do subsequently is to: amplify the CDS do 3' and 5' RACE Clone in a plasmid (do a blunt end or TA cloning) Sequence the insert ...


1

PSI-BLAST creates a protein profile of similar proteins (essentially a scoring matrix based on multiple sequence alignments) that are then used for further DB searches. On the nucleotide level this simply does not make much sense, especially for short sequences. For one, there is much less potential variability which is probably worse for non-coding ...



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