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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


0

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 ...


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 ...


7

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 ...


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 ...


0

At this point, it must be verified experimentally. In this foldit research paper, they use software and user input to design essentially an enhanced version of a naturally occurring protein, but they then physically make their new protein and determine its structure experimentally, using x-ray crystallography. Overall, they use a lot of trial and error ...


1

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


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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 ...


3

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 ...


0

In a liquid chromatography coupled to mass spectrometry (LC-MS) analysis, as analytes elute from the chromatographic column they are sprayed through a hypodermic needle maintained at a high potential difference relative to the mass spectrometer. Combination of this potential difference and the pH of the LC buffers causes the analyte molecules to pick charge. ...


2

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.


1

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.


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 ...


0

There must be some such information, because at the lab we are using the SnapGene software, and it is able to recognize the Ori sequences (and all other sequences). Since it is proprietary software, I doubt they would disclose their list, but others might have the same information. If you really need to find your origin for your plasmid, you could try 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 ...


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 ...


1

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 ...


0

That depends on what your are trying to do. Apparently your query sequence is similar to that of proteins with a known 3D-structure. As it says on Jpred's result page (and help), in this case it might be worth looking at these homologues with experimentally determined structures for information on secondary structure. Most likely it will be more accurate ...


0

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 ...


0

The same question sticked in my mind a month ago. Even @terdon gave an explanatory answer, I want to make a small contribution. When I asked similar question on seqanswers *, one of users gave the link of the study Ashley Lab in Stanford. They generated the "Synthetic major allele human reference genomes". (1) They combined the current reference sequence ...


0

Swiss model is an online tool for modelling protein tertiary and Quaternary structure using evolutionary information. J-pred and Swiss model both are pretty straight forward tools which requires only the sequence. Swiss model requires searching for a template and based on which the protein will be modeled further.J=pred is exclusively used for secondary ...


2

I may be jumping the gun here, but assuming that you haven't searched NCBI or ensembl, I'd do that first. Essentially all genomic information is maintained by a collaboration between US NIH, EU EBI and Japan. All databases are synced to each other, and hence the data should (theoretically) be the same (in practice it never is). I'd suggest you pick one ...


2

For birds you can start by searching 18s in http://birdgenenames.org/cgnc/ But generally NCBI Nucleotide database, should provide you with all information and accession numbers. See this broad search: http://www.ncbi.nlm.nih.gov/nuccore/?term=18S+ribosomal+RNA+gene Adding species specification and other parameters, you might find what you are looking for. ...


0

I strongly suggest you to take a free course on courseraThere are many valid courses focused on bioinformatics for beginners and they offers slides, notes and everything is necessary to start. If you are looking for a nice book to get started, then I suggest you this one



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