LecturesPart06

Rescore these using a scoring similarity 2 matrix and

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Unformatted text preview: ds highest 2. Rescore these using a scoring (similarity) 2. matrix and trim ends that do not contribute to the highest score to x Result: partial alignments without gaps Result: without x Reported as the “init1” score FASTA method 3. Join regions together, including penalties 3. for gaps for x Result: unoptimized alignment with gaps Result: unoptimized x Reported as the “initn” score 4. Use dynamic programming in a band 32 4. residues wide around the best “initn” score residues x Result: optimized alignment with gaps x Reported as the “opt” score Comments on FASTA s Larger k-tuple increases speed since fewer Larger -tuple “hits” are found but it also decreases sensitivity for finding similar but not identical sequences since exact matches of this length are required this Limitations of FASTA s FASTA can miss significant similarity since x For proteins, similar sequences do not have to For share identical residues share 3 Asp-Lys-Val is quite similar to Glu-Arg-Ile yet Glu-Arg-Ile it is missed even with k-tuple size of 1 since no -tuple amino acid matches amino 3 Gly-Asp-Gly-Lys-Gly is quite similar to Gly-Glu-Gly-Arg-Gly but there is only match Gly-Glu-Gly-Arg-Gly with k-tuple size of 1 Limitations of FASTA s FASTA can miss significant similarity since x For nucleic acids, due to codon “wobble”, DNA For sequences may look like XXyXXyXXy where X’s are conserved and y’s are not X’s 3 GGuUCuACgAAg and GGcUCcACaAAA GGcUCcACaAAA both code for the same peptide sequence (Gly-Serboth Thr-Lys) but they don’t match with k-tuple size of 3 Thr-Lys) -tuple...
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