Chapter 3
... algorithm in terms of the number of comparisons used . (and ignoring the time required to compute m= (i j ) / 2 in each iteration of the loop in the algorithm) • Algorithm 3: the binary search algorithm Procedure binary search (x: integer, a1, a2, …,an: increasing integers) i :=1 { i is left end ...
... algorithm in terms of the number of comparisons used . (and ignoring the time required to compute m= (i j ) / 2 in each iteration of the loop in the algorithm) • Algorithm 3: the binary search algorithm Procedure binary search (x: integer, a1, a2, …,an: increasing integers) i :=1 { i is left end ...
I. Comparing genome sequences
... • Homologous sequences = derived from a common ancestor • Orthologous sequences = homologous sequences separated by a speciation event (e.g., human HOXA and mouse Hoxa) • Paralogous sequences = homologous sequences separated by gene duplication (e.g., human HOXA and human HOXB) ...
... • Homologous sequences = derived from a common ancestor • Orthologous sequences = homologous sequences separated by a speciation event (e.g., human HOXA and mouse Hoxa) • Paralogous sequences = homologous sequences separated by gene duplication (e.g., human HOXA and human HOXB) ...
Embedded Algorithm in Hardware: A Scalable Compact Genetic
... Jewajinda, Y. and Chongstitvatana, P.,"FPGA Implementation of a Cellular Univariate Estimation of Distribution Algorithm and Block-based Neural Network as an Evolvable Hardware", IEEE Congress on Evolutionary Computation, Hong Kong, June 1-6, 2008, pp.3365-3372. Jewajinda, Y. and Chongstitvatana, P. ...
... Jewajinda, Y. and Chongstitvatana, P.,"FPGA Implementation of a Cellular Univariate Estimation of Distribution Algorithm and Block-based Neural Network as an Evolvable Hardware", IEEE Congress on Evolutionary Computation, Hong Kong, June 1-6, 2008, pp.3365-3372. Jewajinda, Y. and Chongstitvatana, P. ...
Alignment of pairs of sequences
... Why compare sequences? • To find whether two (or more) genes or proteins are evolutionarily related to each other • To find structurally or functionally similar regions within proteins ...
... Why compare sequences? • To find whether two (or more) genes or proteins are evolutionarily related to each other • To find structurally or functionally similar regions within proteins ...
ppt slides
... Most simple way to decide the top K results of a ranking function like Score (ObjectId) = Linear combinations of attributes is to sort the result and take the top K. This will take nlogn time. Very slow for very large relations where n is quite large. ...
... Most simple way to decide the top K results of a ranking function like Score (ObjectId) = Linear combinations of attributes is to sort the result and take the top K. This will take nlogn time. Very slow for very large relations where n is quite large. ...
Finding motifs in preomoters
... We used the Promoter Database of Saccharomyces cerevisiae. It contains genes and for every gene the TFs that are known to bind its promoter. We took 24 Transcription Factors whose PSWM is known, and 135 promoters of genes which are known to be bound by at least one of them. ...
... We used the Promoter Database of Saccharomyces cerevisiae. It contains genes and for every gene the TFs that are known to bind its promoter. We took 24 Transcription Factors whose PSWM is known, and 135 promoters of genes which are known to be bound by at least one of them. ...
Database Searches for similar sequences
... alignment. Each score links to the corresponding pairwise alignment between query sequence and hit sequence (also referred to as subject sequence). 3 - E Value (Expect Value) describes the likelihood that a sequence with a similar score will occur in the database by chance. The smaller the E Value, ...
... alignment. Each score links to the corresponding pairwise alignment between query sequence and hit sequence (also referred to as subject sequence). 3 - E Value (Expect Value) describes the likelihood that a sequence with a similar score will occur in the database by chance. The smaller the E Value, ...
Molecular-aided identification of woody plants in a tropical forest of
... Blaxter, M., et al. 2005 Defining operational taxonomic units using DNA barcode data Phil. Trans. R. Soc. B ...
... Blaxter, M., et al. 2005 Defining operational taxonomic units using DNA barcode data Phil. Trans. R. Soc. B ...
Instructor Rubric for Presentations
... Directions To Evaluator: Please fill in each of the blank spaces (either during the presentation, or afterwards) based on what is presented by your peer. This sheet can also be used as a study-guide for yourself, later on. ...
... Directions To Evaluator: Please fill in each of the blank spaces (either during the presentation, or afterwards) based on what is presented by your peer. This sheet can also be used as a study-guide for yourself, later on. ...
Sequence Alignment
... • Exactly same Nucleotide/AminoAcid in same position Sequence similarity • Substitutions with similar chemical properties Sequence homology • General term that indicates evolutionary relatedness among sequences • Sequences are homologous if they are derived from a common ancestral sequence. ...
... • Exactly same Nucleotide/AminoAcid in same position Sequence similarity • Substitutions with similar chemical properties Sequence homology • General term that indicates evolutionary relatedness among sequences • Sequences are homologous if they are derived from a common ancestral sequence. ...
Why BLAST is great - GENI
... programming” algorithms such as SmithWaterman for detecting weak similarity In practice, they run much faster and are usually adequate The BLAST program developed by Stephen Altschul and coworkers at the NCBI is the most widely used heuristic program. Altschul SF, Madden TL, Schäffer AA, Zhang J, ...
... programming” algorithms such as SmithWaterman for detecting weak similarity In practice, they run much faster and are usually adequate The BLAST program developed by Stephen Altschul and coworkers at the NCBI is the most widely used heuristic program. Altschul SF, Madden TL, Schäffer AA, Zhang J, ...
BLAST seminar
... – If sequences are related by divergence from a common ancestor, there are said to be homologous. ...
... – If sequences are related by divergence from a common ancestor, there are said to be homologous. ...