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Comparing biological sequences (3): Database searching and Multiple alignment

Comparing biological sequences (3): Database searching and Multiple alignment. Database searching. Goal: find similar (homologous) sequences of a query sequence in a sequence of database Input: query sequence & database Output: hits (pairwise alignments). Database searching.

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??? ?????. ??????? ??????? ?????? ??? ?????? ( ???? ???? ???? ?????? ). Subroutines Revision. Defining a subroutine. sub reverseComplement { # read string # reverseComplement it # return it }. sub SUB_NAME { # Do something ... }. Subroutines Revision. Invoking a subroutine.

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A practical approach

DB Web addresses. A practical approach. Searching the primaries. Searching the secondaries. Significance of database matches. Software Web addresses. Why Search Databases?. To find out if a new DNA sequence already is deposited in the databanks.

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Heuristic Approaches for Sequence Alignments

Heuristic Approaches for Sequence Alignments. Outline. Sequence Alignment Database Search FASTA BLAST. Sequence Alignment. Dynamic Programming (give optimal solution(s)) Needleman-Wunsch (Global Alignment) Smith-Waterman (Local Alignment) Heuristics (give approximate solution(s))

575 views • 37 slides

Applied Bioinformatics

Applied Bioinformatics. Week 4. Similarity Searching. Heuristic Algorithms FASTA BLAST. FASTA Algorithm. Algorithm? Pearson and Lipman 1988. FASTA - Algorithm -. High level algorithm Let q be a query max ? 0 For each sequence, s in DB compare q with s and compute a score, y

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Pyrosequencing for Metagenomics: accessing and organizing raw data

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Improved tools for biological sequence comparison

Improved tools for biological sequence comparison. Author : WILLIAM R. PEARSON, DAVID J. LIPMAN Publisher: Proc. Natl. Acad. Sci. USA 1988 Presenter: Hsin-Mao Chen Date: 2010/04/28. Outline. Introduction Step 1 Step 2 Step 3 Step 4 Result. Introduction. A heuristic method.

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Advanced Exercises

336 views • 11 slides