1. Chapter 3 Ying Xu

6. Total numbers of occurrences of X in coding and noncoding regions. Relative frequency (RF)of X in coding regions = number of occurrences of X / total number in coding regions Est. RF of X in non-coding regions in a similar fashion.

8. Overall preference value = sum of all preference values of the di-codons. Positive preference value -> coding region Negative preference value -> noncoding region. GRAIL AND SORFIND, GRAIL AND SORFIND, HIDDEN MARKOV MODELS, HIDDEN MARKOV MODELS,

17. A non-gene is a region in an ORF that does not overlap any coding regions set A contains only genes and set B contains only non-genes, Examine the common features of sets A & B

20. Input Nodes Output node Hidden layer

22. Conserved (long) regions across multiple genomes, (a) megaBLAST(b) SENSEI(c) MUMmer Very long sequence comparisons. First find short (size of 8) ungapped sequence matches. Sequences to be aligned are closely related. Speed up computational time and reduce the memory requirement. Extend them into longer gapped alignments. Utilizing a suffix trees data structure.

23. Genome A Genome B Genes

25. Cont.,

29. Cont., `

38. (1) Predicte promoter region and a terminator, (2) Set of genes arranged in tandem on the same strand, (3) Functional information of the genes involved. Identify transcriptional regulatory networks

41. Cont.,

53. Modeled Genes, Functional Assignments, RNA genes, Repeats, General Sequence Features.

57. Is an open source annotation tool for microbial genomes,

58. Ab intio and computational approach, Models for prediction, Evaluation, Large-scale annotation efforts, RNA-coding genes and its prediction, Promoter – Structure and function of each gene Operon –Basic unit of genes, Genome-Scale gene mapping and pathway analysis