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10

Overview Modelling has come on leaps and bounds over the last decade or so and in many cases has acted as a sometimes viable, and inexpensive substitute for experimental structures. How do you know when you get it right? Ultimately, one still needs experimental evidence to know when a model generated in silico is right. But there are ways of scoring ...


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My understanding of those three words as follows: sequence is a generic name describing order of biological letters (DNA/RNA or amino acids). Both contigs and reads are DNA/RNA or aa sequences reads are just a short hand for sequenced reads. Usually sequenced reads refer to somewhat digital information obtained from the sequencing machine (for example ...


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Bearing in mind that the information is bound to be incomplete (as is the list of existing species), you could use the NCBI taxonomy database. For example, checking the page for the Drosophila genus will give you an idea of its size. For more precise numbers, you can download the taxdump.tar.gz file from NCBI's FTP server (link), extract it and run the ...


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Have you discovered wormbase yet? It will become your new best friend. In worms gene names reflect the loss-of-function (lf) phenotype. Daf means "abnormal DAuer Formation," so daf-2 was the second daf gene identified (ref). The mutations are called alleles and each worm lab has their own allele designation. e was for England and in that lab's strain list ...


3

RAM's answer is very good, I'll just add on the computational side, short reads are error prone. That's important to account for when aligning or assembling. The reads themselves can just be inaccurate, which we detect by having multiple reads overlapping by a lot; we assume that stray discrepancies seen in only a single read at a position are errors. ...


3

Here's a quick summary of a few mis-hits in your otherwise good analysis: Not many bioinformatics applications use Hadoop, Apache Spark or Apache Flink. In fact, I have never heard of the Apache Spark and Flink tools, and I've seen only 2 people use Hadoop to process alignment files. Reads are not "converted" real, physical DNA. They are representations ...


3

The equation in the OP has been updated to $(y-a)^2(y-a\theta)$ which yields the correct expansion. Therefore, by equating the coefficients, we obtain \begin{align} \alpha &= (2+\theta)a\tag{1}\\ \rho/\beta^2 &= a^2(1+2\theta)\tag{2}\\ \alpha/\beta^2 &= a^3\theta\tag{3} \end{align} Using equations (1) to (3), we get the desired $\rho$ and ...


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501 denotes 501st residue in the corresponding PDB entry — 1BDG. See here A single protein can have multiple cavities (see here) and the multiple entries denote centres of different cavities.


3

I'm going to say the same thing as @Serine but in a slightly different context. Let's take an example where you want to compare smoking persons against non-smokers. In this context, you'd want to take a DNA sequence of smoking persons. However, due to technology limitation you won't get a single DNA sequence from the sequencing machine. You'll get millions ...


2

Often genes or other DNA fragments are inserted into an expression vector and used to transform bacteria or other cells. When a mixture of vectors is used containing various DNA fragments (e.g. a chopped-up genome), then individual (bacterial) colonies need to be isolated to make sure they carry only one insert. This can be done, e.g., by plating the ...


2

Contig or scaffold N50 is a weighted median statistic such that 50% of the entire assembly is contained in contigs or scaffolds equal to or larger than this value. Mathematically: Given a set of sequences of varying lengths, the N50 length is defined as the length N for which 50% of all bases in the sequences are in a sequence of length L < N. ...


2

To find out whether a dataset was paired-end or single-end, go to SRA, click on a run, and look under "Library". Paired-end datasets will typically have "Layout: paired". Note that people don't always mark this correctly, which causes no end of headaches. Regarding lines like "CCCFFFFFGFHHHGJJJJI#1?FEIGGI", that's the quality score line. Look at the fastq ...


2

Direct comparison of the course would be difficult between tissues and cultured cells. In stead of time scale, you might want to use markers. For example, Kislinger et al. show the expression peak of SIX1 is 2 days after differentiation; SMAD3, 4 days. I am not a right person who can tell which markers are good, but I believe you could find more information ...


1

I'd just compare the amino acid sequences of the individual protein chains. With some leeway for residues not observed in the density, ie only require 90 or 95% sequence identity, or ignore gaps. This will not tell you anything about whether the dimer (if you observe several molecules in the asymmetric unit) is actually real. For that, you'd need to do an ...


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You can try http://timetree.org/ to get the divergence time if you already have the names of the taxa.


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Maybe you could get some information from the Angiosperm Phylogeny Group: http://www.mobot.org/MOBOT/research/APweb/ They even have a tree where model organisms are highlighted: http://www.mobot.org/MOBOT/research/APweb/trees/modeltreemap.html


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If you know the species name, you can search TreeBase to find previously published phylogenetic trees which will point you towards close relatives to your species. Depending on how obscure your taxon is, though, you might not find much.


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In general, a read simulator does the following: Selects regions from a reference sequence with some sort of predefined or user-specified size distribution. Converts the sequence from those regions into single or paired end reads with quality scores. The quality scores and read lengths are typically user defined. Introduces errors into the aforementioned ...


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As you can find under the table with cavity centers in pdf version of this article: The table lists the protein’s PDB ID, the ligand considered and the specified cavity center. 22 ligands are similar to hexoses in shape and/or size. The cavity center is the centroid of the reported PDB atom numbers. And a little later: The binding-site center is ...


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3D structure. Use the PDB to identify structures that are similar to the one you have found (you can use BLAST to search the PDB). A 30% match or above is usually acceptable, and multiple alignments are of course useful at lower match scores. If structures exist that are similar enough, you can use homology modelling to generate a 3D structure (this is what ...


1

Assuming each gene symbol represents a unique gene or protein (this may not be true; see for gene name aliases in e.g. NCBI Entrez gene) you can get a lot of information programmatically. Below is an example using R and Bioconductor resources. Define your list of genes: # list of gene symbols, here we focus on one. > genes <- "KRAS" Load the ...


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You may create a new database with the new sequences and create an alias linking the old and new databases with blastdb_aliastool



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