'Query sequence' presentation slideshows

General nucleic acid Sequence databases

General nucleic acid Sequence databases. EMBL :(European Molecular Biology Laboratory) http://www.ebi.ac.uk/Information/ GenBank : NCBI (National Center for Biotechnology Information) http://www.ncbi.nlm.nih.gov/ DDBJ : DNA Data Bank of Japan

1.91k views • 142 slides

Family of HMMs

Family of HMMs. Nam Nguyen University of Texas at Austin. Outline of Talk. Background Family of HMMs Model Alignment algorithm Applications of fHMM SEPP (Mirarab, Nguyen, and Warnow. PSB 2012) TIPP (Nguyen, et al. Under review) Conclusions and future work. Phylogenetics.

1.34k views • 116 slides

CONT

Outline 1.what is BLAT & why we need it 2.BLAT's similarity & difference compared with BLAST 3.BLAT's application forms 4.BLAT's 3 major application 5. conclusion.

1.03k views • 82 slides

TEMA 6

1.11k views • 68 slides

Database Searching

Database Searching. BLAST and FastA. Database Homology Searching. Use algorithms to increase efficiency and provide a mathematical basis for searching which can be translated into statistical significance Assumes that sequence, structure and function are interrelated.

899 views • 58 slides

BCB 444/544

BCB 444/544. Lecture 10 BLAST Details Plus some Gene Jargon #10_Sept12. Required Reading ( before lecture). ? Mon Sept 10 - for Lecture 9 BLAST variations; BLAST vs FASTA, SW Chp 4 - pp 51-62 ? Wed Sept 12 - for Lecture 10 & Lab 4 Multiple Sequence Alignment (MSA)

752 views • 57 slides

Bioinformatics Tools

Bioinformatics Tools. Stuart M. Brown, Ph.D Dept of Cell Biology NYU School of Medicine. Stuart M. Brown, Ph.D Dept of Cell Biology NYU School of Medicine. Bioinformatics Tools. Overview.

1.13k views • 50 slides

Biology 4900

Biology 4900. Biocomputing. Chapter 3. Pairwise Sequence Alignment. Comparing protein sequences. Comparing protein sequences usually more informative than nucleotide sequences. Why? Changing base at 3 rd position in codon does not change AA ( Ex: Both UUU and UUC encode for phenylalanine )

474 views • 36 slides

Dot Plots, Path Matrices, Score Matrices

Dot Plots, Path Matrices, Score Matrices. Sequence A. V. T. R. I. V. H. V. N. S. I. L. P. S. T. N. I. L. S. V. I. L. S. T. R. I. Sequence B. V. I. L. P. E. F. S. T. diagonal lines give equivalent residues. Sequence A. V. T. R. I. V. H.

490 views • 35 slides

An Introduction to Bioinformatics

An Introduction to Bioinformatics. Database Searching - Pairwise Alignments. AIMS. To explain the principles underlying local and global alignment programs To explain what substitution matrices are and how they are used To introduce the commonly used pairwise alignment programs

416 views • 34 slides

Computing in Molecular Biology

Computing in Molecular Biology. Hugues Sicotte National Center for Biotechnology Information sicotte@ncbi.nlm.nih.gov. Alignment methods. Sequence Alignment representation using a dot plot. For a query of N letters against a subject sequence of M letters, it requires MxN comparisons.

470 views • 34 slides

Bioinformatics

Bioinformatics. Bioinformatics. Bioinformatics is an applied science that uses computer programs to access molecular biology databanks to make inferences about the information contained within the data archives.

1.12k views • 32 slides

Time Series Sequence Matching

471 views • 30 slides

Parsing BLAST output

498 views • 24 slides

Heuristic Methods for Sequence Database Searching

Heuristic Methods for Sequence Database Searching. BMI/CS 576 www.biostat.wisc.edu/bmi576/ Colin Dewey cdewey@biostat.wisc.edu Fall 2010. query. database. www.ncbi.nlm.nih.gov/BLAST/. BLAST Results. BLAST Programs. Heuristic Alignment Motivation.

376 views • 23 slides

Alignment of Long Sequences: LAGAN

Alignment of Long Sequences: LAGAN. BMI/CS 776 www.biostat.wisc.edu/bmi776/ Spring 2019 Colin Dewey colin.dewey@wisc.edu. These slides, excluding third-party material, are licensed under CC BY-NC 4.0 by Mark Craven, Colin Dewey, and Anthony Gitter. Goals for Lecture. Key concepts

1.4k views • 21 slides

CISC 667 Intro to Bioinformatics (Spring 2007) Sequence pairwise alignment

CISC 667 Intro to Bioinformatics (Spring 2007) Sequence pairwise alignment. Score statistics: E-value and p-value Heuristic algorithms : BLAST and FASTA Database search : gene finding and annotations. Significance of scores Goals for sequence alignments: (1) whether and

326 views • 21 slides

Distributed BLAST with ProActive

Distributed BLAST with ProActive. Santosh Anand Richard Christen* Claude Pasquier* *UMR 6543 CNRS & University of Nice Virtual Biology Lab, Campus Valrose. Plan. Sequence Similarity Search Problem and BLAST: Overview and Issues Parallel Distributed BLAST: Various Approaches

325 views • 17 slides

Author: Khaled Benkrid; Ying Liu; AbdSamad Benkrid Publisher:

A HIGHLY PARAMETERIZED AND EFFICIENT FPGA-BASED SKELETON FOR PAIRWISE BIOLOGICAL SEQUENCE ALIGNMENT. Author: Khaled Benkrid; Ying Liu; AbdSamad Benkrid Publisher: IEEE TRANSACTIONS ON VERY LARGE SCALE INTEGRATION (VLSI) SYSTEMS 2009 Presenter: Chin-Chung Pan Date: 2010/05/12. OUTLINE.

286 views • 17 slides

BLAST addendum

132 views • 4 slides