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There is a difference between animals in their requirements for amino acids. For example, cats need high amounts of taurine (and can't make it) and when fed diets lacking enough can go blind. This is why vegans trying to feed vegan diets to their pets can be very bad for the pet. Animal proteins have sufficient taurine for the cat. However, the meat of a ...


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That is a very bad test case. The problem is that the sequences are too short and involve a long repetition. This means that the default gap penalties and the gap-length penalties are not applicable. They are designed to work with longer sequences, where the penalty of inserting a gap can be offset by an increase in matches. In any case you can get bad ...


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Your guess is made without knowing protein substitution probabilities. Optimality of alignment in BLAST is a metrics of the scoring function. The scoring function depends on the word size (length of the seed that initiates an alignment), rewards and penalties for matches and mismatches - gap cost and substitution matrix. In general, BLAST uses BLOSSUM and ...


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Needleman-Wunsch does an end-to-end (global) alignment (BLAST uses Smith-Waterman). Needle from the EMBOSS toolkit performs Needleman-Wunsch alignment. It will report the highest scoring alignment. I am not sure which alignment it reports when there are two of them with equal scores (I don't think it is random). I just tried your case: replaced B with W as ...


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Decreasing the number of essential amino acids is frequently used as a selection marker during molecular biology experiments: An organism (usually yeast) that cannot synthesize a certain amino acid is first grown in the presence of said amino acid in the media. Then it is transfected with a gene of interest together with the gene that enables it to ...



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