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4

There are some tools for predicting the binding: TargetScan (based on seed match [primary], extra pairing, sequence context 1 — nucleotide composition around the site etc [secondary]) miRanda (based on hybridization stability and seed match[primary] and sequence context [secondary]) PicTar (adds a layer of evolutionary conservation criteria) 1 Context ...


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Your logic on the problem seems correct. The wikipedia article about the Hamming distance describes both a python and a C implementations. The python version assumes two strings of equal length: def hamming_distance(s1, s2): #Return the Hamming distance between equal-length sequences if len(s1) != len(s2): raise ValueError("Undefined for ...


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Bioinformatics journals can deal perfectly with this type of papers. If you target a journal like Bioinformatics, then you can be as technical as you want (and you probably should). Biologists that read those journals will most likely understand the terminology. Even traditional experimental biology journals, like Nucleic Acids Research, now include a ...


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Sequences that don't appear in a genome are called "nullomers". That article claims that there are no 10bp sequences that don't appear in the human genome, and 80 11bp sequences that don't, citing this paper.


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Every amino acid has a different isoelectric point: a pH where they do not carry electric charge. This isoelectric point depends on the side chains: By glycine the side chain -H is neutral (while the amino and carbonic acid groups are not) so the IEP is 5.97. By lysine the side chain -(CH2)4-NH2 is alkaline (R-NH2 + H+ <-> R-NH3+), so it will have a ...


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Yes, it is possible to sequence a specific region of the genome. The method, as you mentioned, is called targeted sequencing. Resequencing is basically sequencing something that has already been sequenced. This means that instead of assembling all of your sequence reads from scratch, you can just align them to the reference sequence (in your case, the entire ...


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I would thoroughly check the literature on the UTR you are interested in, a lot of this has already been done for many genomic regions since nextgen seq began. You will want to first off use computational prediction algorithms to help guide you in getting a good Candidate list of miRNAs The interaction between a miRNA and its target mRNAs is usually ...


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As Chris mentioned in his comment, 'printing' DNA from scratch (i.e. synthesizing a long strand de novo) is expensive and difficult. Unfortunately, the process of GMO creation is not as simple as assembling a beautiful DNA sequence on the computer, printing it, and then inserting it into a cell. Here's a related question about de novo sequencing. Plant ...


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Here a solution that does not require you to upload the files to the servers: You can graphically visualize DSSP and Stride at the Sequence Page at RCSB PDB: http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=5P21&bionumber=1 "add annotation" -> Stride and look at the graphical comparison between DSSP and Stride.


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This is an important topic in immunology, especially for vaccine development. MHC or HLA is a molecule expressed by some cells of the immune system which acts like a "catcher's mitt" and "presents" short snippets of protein to other immune cells. Other molecules act alongside MHC to provide co-signals which promote or suppress immune attack against the ...



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