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How Blast Works Role of Word Size, T, & Scoring Matrix in Seeding

Explore the impact of word size, scoring matrix, and extensions on BLAST algorithm through examples and analysis. Learn to optimize query seeding and evaluation for efficient sequence alignment.

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How Blast Works Role of Word Size, T, & Scoring Matrix in Seeding

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  1. How Blast WorksRole of Word Size, T, & Scoring Matrix in Seeding Query: METGAAAALGMALAAGLGALGAAIGDGICTSKLLEGVARQPEARGQLMTLMFISVGLIESIPIIAVVVAFMLMGKIA Database entry#1: MEVGAAAAIATGLAVGLGALGAAVGDGICTGKAIESIARQPEAKGTIQTTMFISVGLIESIPIIAVVLAFMLFGKLG Database entry#2: MEIVLGMTAIAVALLIGMGALGTAIGFGLLGGKFLEGAARQPEMAPMLQVKMFIVAGLLDAVTMIGVGIALFMLFTNPLGAML Database entry#3: MDMSLQVLGNLNGLTAVAVALLISLPALGTAIGFGVLGGKYLEGVARQPELGGMLLGRMFIVAAFVDAFAAISIAIGFLVLYANPLAIPGLAETAQKVIGS • Assume a word size of 3, T = 999, & Blosum62 matrix. • How many word hits to database entry #1, #2, & #3? • (2) Does entry #3 look better if we lower word size to 2? • (3) Does entry #3 look better if T = 10?

  2. How Blast WorksRole of X in Extension Query: METGAAAALGMALAAGLGALGAAIGDGICTSKLLEGVARQPEARGQLMTLMFISVGLIESIPIIAVVVAFMLMGKIA Database entry#1: MEVGAAAAIATGLAVGLGALGAAVGDGICTGKAIESIARQPEAKGTIQTTMFISVGLIESIPIIAVVLAFMLFGKLG Database entry#2: MEIVLGMTAIAVALLIGMGALGTAIGFGLLGGKFLEGAARQPEMAPMLQVKMFIVAGLLDAVTMIGVGIALFMLFTNPLGAML Database entry#3: MDMSLQVLGNLNGLTAVAVALLISLPALGTAIGFGVLGGKYLEGVARQPELGGMLLGRMFIVAAFVDAFAAISIAIGFLVLYANPLAIPGLAETAQKVIGS • Try to extend off of the seed shown in red using X = 5. • (2) Try to extend off of the seed shown in red using X = 2.

  3. How Blast WorksRole of Scoring Matrix in Evaluation Query 8 ALGMALAAGLGALGAAIGDGICTSKLLEGVARQPEARGQLMTLMFISVGLIESIPIIAVV 67 A+ +AL G+GALG AIG G+ K LEG ARQPE L MFI GL++++ +I V Sbjct 9 AIAVALLIGMGALGTAIGFGLLGGKFLEGAARQPEMAPMLQVKMFIVAGLLDAVTMIGVG 68 Query 68 VA-FML 72 +A FML Sbjct 69 IALFML 74 • Score the alignment above with the Blosum62 matrix, and Gap Penalties (Existence: 15, Extension: 2). • (2) How would the score change if you only scored up to the end of the first line?

  4. How Blast WorksTry It For Yourself METGAAAALGMALAAGLGALGAAIGDGICTSKLLEGVARQPEARGQLMTLMFISVGLIESIPIIAVVVAFMLMGKIA • Blast against the nr database of proteins. • Blast against just the microbial genome (proteins) database. • Blast against just the Desulfutomaculum reducens genome.

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