How is sequence similarity different than percent identity from BLASTP? Entering edit mode 23 months ago Viraj • 0 Hi Everyone, I am new to Biostars. I am having trouble finding a concrete answer to the post's question. My understanding is that sequence similarity is the fraction of residues that are similar between two different protein sequences. Percent identity is the number of characters that match exactly between two different sequences. I read that sequence similarity is strongly correlated to percent identity. I also read that it is a subset of percent identity. These two are contradicting. Can someone help me distinguish between the two concepts? Thanks hom*ology BLASTP • 7.7k views ADD COMMENT • link 23 months ago by Viraj • 0 Entering edit mode Thank you for the link. Looking at the link and these sequences: A: AAGGCTT B: AAGGC I understand this has 100% identity. How is this 60% similar? Edit distance is minimal number of edit operations (inserts, deletes, and substitutions) in order to transform the one sequence into an exact copy of the other sequence being aligned Similar = 1 - edit distance/ unaligned length of shorter sequence Therefore, similar = 1 - (2/2) or 1. Not sure how the author got 60%. Either the author made a typo in the similar definition or the math is wrong. Can someone explain? Thanks. ADD REPLY • link 23 months ago by Viraj • 0 1 Entering edit mode 23 months ago Mensur Dlakic ★ 28k Sequence identity has a literal meaning that should be easy to understand. When the two sequences are aligned, any pair of residue is either identical, or it isn't. Sequence similarity is a broader term, and always includes identity. That means identical residues are always similar by definition, while the opposite is not necessarily true. Therefore, sequence similarity is equal to or greater than sequence identity. Similarity includes conservative substitutions that usually have positive scores in substitution matrices. The alignment below has 430/432 identical residues (see under ADD COMMENT • link 23 months ago by Mensur Dlakic ★ 28k Entering edit mode Thank you for the comprehensive answer! This means sequence similarity is the positive score and sequence identity is the identity score from BLAST ADD REPLY • link 23 months ago by Viraj • 0 Entering edit mode This means sequence similarity is the positive score and sequence identity is the identity score from BLAST Not quite. Sequence identity is a fraction of identical residues, and similarity is a fraction of similar residues. BLAST provides a single score that includes everything rather than breaking it down by identity or similarity. ADD REPLY • link 23 months ago by Mensur Dlakic ★ 28k Entering edit mode In your above example, identical residues is 430/432 and similar residues is 432/432. Similar residues include identical residues plus similar residues denoted as a plus. This is not right? ADD REPLY • link 23 months ago by Viraj • 0 1 Entering edit mode It is right, but they are not scores in the same sense as bit-score. They are fractions. ADD REPLY • link 23 months ago by Mensur Dlakic ★ 28k Entering edit mode I see. Thank you for your answers and clarification. I appreciate the help! ADD REPLY • link 23 months ago by Viraj • 0 Identities) and 432/432 similar residues (see under Positives). If you look in the middle alignment row, similar residues have a + sign instead of residue letters (around positions 285 and 340). If the residues were not similar, there would be an empty space instead of +.Score Expect Method Identities Positives Gaps877 bits(2265) 0.0 Compositional matrix adjust. 430/432(99%) 432/432(100%) 0/432(0%)Query 1 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK 60 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKSbjct 1 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK 60Query 61 HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD 120 HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDSbjct 61 HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD 120Query 121 RIRKLADQCTGLQGFLVFHsfgggtgsgftsLLMERLSVDYGKKSKLEFSIYPAPQVSTA 180 RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTASbjct 121 RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA 180Query 181 VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA 240 VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASbjct 181 VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA 240Query 241 SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN 300 SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQL+VAEITNACFEPANSbjct 241 SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLTVAEITNACFEPAN 300Query 301 QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP 360 QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKR+IQFVDWCPTGFKVGINYQPPSbjct 301 QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPP 360Query 361 TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE 420 TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSESbjct 361 TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE 420Query 421 AREDMAALEKDY 432 AREDMAALEKDYSbjct 421 AREDMAALEKDY 432
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