B o b G r o s s , B i o 3 9 / 1 3 9Comparing SequencesB o b G r o s s , B i o 3 9 / 1 3 9Why Do Sequence Comparisons?look for similarity between sequence pairslook for similarity among many sequences - define a consensussearch databases for other related sequenceslearn about possible functional properties through similarity with other sequences having a known functioninfer evolutionary relationshipsB o b G r o s s , B i o 3 9 / 1 3 9Some DefinitionsIdentity - When corresponding characters in two different sequences are the same in each position along the sequences, the sequences are said to be identical. Similarity -! The degree to which sequences share identities. Homologs - Similar sequences that have common origins but may or may not have common activity. Orthologs - Homologs produced by speciation. They represent genes derived from a common ancestor that diverged due to divergence of the species. They tend to have similar function.Paralogs - Homologs produced by gene duplication. They represent genes from a common ancestor that duplicated within an species and then subsequently diverged. They tend to have different functions.B o b G r o s s , B i o 3 9 / 1 3 9Defining SimilarityB o b G r o s s , B i o 3 9 / 1 3 9Defining Similaritytheir vs. thereB o b G r o s s , B i o 3 9 / 1 3 9Defining Similaritytheir vs. therehere vs. thereB o b G r o s s , B i o 3 9 / 1 3 9Defining Similaritytheir vs. therehere vs. thereI will assemble the bicycleB o b G r o s s , B i o 3 9 / 1 3 9Defining Similaritytheir vs. therehere vs. thereI will assemble the bicycle I will not assemble the bicycleB o b G r o s s , B i o 3 9 / 1 3 9Defining Similaritytheir vs. therehere vs. thereI will assemble the bicycle I will not assemble the bicycle I will disassemble the bicycleB o b G r o s s , B i o 3 9 / 1 3 9Defining Similaritytheir vs. therehere vs. thereI will assemble the bicycle I will not assemble the bicycle I will disassemble the bicycle I will assemble the bikeB o b G r o s s , B i o 3 9 / 1 3 9Defining Similaritytheir vs. therehere vs. thereI will assemble the bicycle I will not assemble the bicycle I will disassemble the bicycle I will assemble the bikegreenyellowbluehouseB o b G r o s s , B i o 3 9 / 1 3 9Defining Similaritytheir vs. therehere vs. thereI will assemble the bicycle I will not assemble the bicycle I will disassemble the bicycle I will assemble the bikegreenyellowbluehouseLys vs. ArgorLys vs. PheB o b G r o s s , B i o 3 9 / 1 3 9Dot Matrix Comparisonscompares two sequences graphicallyuses a double sliding window approachprovides immediate visual feedback of similaritiesvery sensitive to parameters usedB o b G r o s s , B i o 3 9 / 1 3 9dog vs. rat chymotrypsin cDNAWindow = 10Mismatches = 0B o b G r o s s , B i o 3 9 / 1 3 9dog vs. rat chymotrypsin cDNAWindow = 10Mismatches = 2B o b G r o s s , B i o 3 9 / 1 3 9dog vs. rat chymotrypsin cDNAWindow = 20Mismatches = 5B o b G r o s s , B i o 3 9 / 1 3 9Dot Matrix - Color Conveys InformationWindow = 10 Mismatches = 0 Mismatches = 1 Mismatches = 2B o b G r o s s , B i o 3 9 / 1 3 9Window = 10 Mismatches = 0 Mismatches = 1 Mismatches = 2B o b G r o s s , B i o 3 9 / 1 3 9Dot Matrix - cDNA vs Genomic DNAWindow = 10 Mismatches = 0 Mismatches = 1 Mismatches = 2B o b G r o s s , B i o 3 9 / 1 3 9Ribosomal DNA Dot Matrix#1Window = 10 Mismatches = 0 Mismatches = 1 Mismatches = 2B o b G r o s s , B i o 3 9 / 1 3 9Ribosomal DNA Dot Matrix#2Window = 15 Mismatches = 0 Mismatches = 3 Mismatches = 5B o b G r o s s , B i o 3 9 / 1 3 9Dot Matrix (Protein - Identity Table)Window = 10 Mismatches = 0 Mismatches = 3 Mismatches = 5B o b G r o s s , B i o 3 9 / 1 3 9PAM250 TableAla Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr ValXAla 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0Arg -2 6 0 -1 -4 1 -1 -3 2 -2 3 3 0 -4 0 0 -1 2 -4 -2 -1Asn 0 0 2 -4 0 2 -2 -3 1 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 0Asp 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 -1Cys -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -3Gln 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 -1Glu 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 -1Gly 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 -1His -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 -1Ile -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -1Leu -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -1Lys -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 -1Met -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -1Phe -3 -4 -3 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -2Pro 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1Ser 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0Thr 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0Trp -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -4Tyr -3 -4 -2 …