1. EMBOSS GUI 2k81217

2. EMBOSS http://bioinfo.nhri.org.tw/

3. EMBOSS  Command Mode EMBOSS - functions complete - establish personal database - Unix interface  JEMBOSS - HTML interface, personal account required - functions limited - java windows  EMBOSS GUI - concise, easy to use - Web browser, no account needed

4. EMBOSS GUI http://bioinfo.nhri.org.tw/gui/

5. EMBOSS GUI http://bioinfo.nhri.org.tw/gui/

7. Find programs by keywords

9. html

10. Displays a program's help documentation manual

13. Additional web sites of EMBOSS http://bioweb.pasteur.fr/seqanal/EMBOSS/ http://csc-fserve.hh.med.ic.ac.uk/emboss.html

14. Tools in EMBOSS  Sequence analysis: RE MAP, ORF, translation, GC content REMAP, GETORF, PLOTORF, GEECEE  Sequence alignment: NEEDLE, WATER, EMMA, SHOWALIGN, PRETTYPLAT  Scans DNA sequences for transcription factors: TFSCAN  Function prediction: Motif and Profiles PATMATMOTIFS  Protein 2D structure: HELIXTURNHELIX TMAP

15. Restriction Enzyme MAP REMAP

16. Restriction cutting sites translation

17. Enzyme cutting frequency

19. Finds and extracts open reading frames (ORFs) GETORF

20. Finds and extracts open reading frames (ORFs) GETORF

21. Plot potential open reading frames PLOTORF

22. Plot potential open reading frames PLOTORF

23. Calculates fractional GC content of nucleic acid sequences GEECEE

24. Calculates fractional GC content of nucleic acid sequences GEECEE

25. Sequence alignment  Global alignment: compare the whole similarity and length of two sequence NEEDLE  Local alignment: find a most identical/similarity region of two sequence WATER  multiple sequence alignment: EMMA, SHOWALIGN, PRETTYPLAT

26. Global alignment NEEDLE Sequence 1 Sequence 2

27. Global alignment NEEDLE

28. Local alignment WATER Sequence 1 Sequence 2

29. Local alignment WATER

30. Multiple sequence alignment EMMA

31. Multiple sequence alignment EMMA copy

32. Displays a multiple sequence alignment SHOWALIGN

33. Displays a multiple sequence alignment SHOWALIGN Identical sequence

34. Displays aligned sequences, with colouring and boxing PRETTYPLOT

35. Displays aligned sequences, with colouring and boxing PRETTYPLOT

36. http://www.ensembl.org/index.html

37. http://www.ensembl.org/info/websit e/archives/index.html

40. ENSMUSG00000057967

41. Select Ensembl database

47. Scans DNA sequences for transcription factors TFSCAN

48. Scans DNA sequences for transcription factors TFSCAN

49. http://www.cbrc.jp/research/db/TFSEARCH.html

51. Minus strand Plus strand

52. http://www.cbil.upenn.edu/cgi-bin/tess/tess?RQ=SEA-FR- QueryS

53. copy & paste again and again

59. 練習 試問 FGF2, FGF3, FGF4, FGF8, and FGF9 是否可被 CREB 調控？

60. Whole Genome Search of Candidate Genes by Profile Hidden Markove Model

61. The Binding Element Searching Tool (THE BEST)  Users could build up a customized hidden markov model (HMM) via HMMER program by upload or paste a set of element sequences containing specific transcription factor binding site (in FASTA format) and use this model to search the multi-species promoter region (human, mouse and rat) retrieved from the EnsMart system annotated by ensembl project

62. Motivation  Search for novel regulated target genes by known transcription factor binding sites (ex. ERE) based on multiple alignments Literature search （ promoter activity 、 gel shift assay 、 ChIP ）

63. Searching Platform  Hidden Markov Model based search tools Promoter EnsMart Promoter sequence HMMER2.2g Pattern ClustalW Calibrate Build Search Know EREs HMMER2.2g ERE_DB

64. http://www.binfo.ncku.edu.tw/

65. http://thebest.binfo.ncku.edu.tw/thebest/

71. StAR

74. 練習  利用之前的練習，找出約 20 條 CRE 的 sequences （需包含 5‘ 與 3’ flanking sequences ，約 20bp 左右），以 FASTA format 輸入 THE BEST 進行分析，並找出 10 個 candidate genes

75. Search a PROSITE motif PATMATMOTIFS

76. Search a PROSITE motif PATMATMOTIFS

77. nucleic acid binding motifs HELIXTURNHELIX

78. nucleic acid binding motifs HELIXTURNHELIX

79. Displays membrane spanning regions TMAP

80. Displays membrane spanning regions TMAP

81. Homework 將序列 AB009865 利用 Emboss 來分析此序 列各種特性（ ORF,, transcription factors, motif 等 ) 。請將你的結果連同說明在 12 月 21 日 23:59:59 前放上你的個人網頁。 將序列 AB009865 利用 Emboss 來分析此序 列各種特性（ ORF, restriction enzyme cutting sites, transcription factors, motif 等 ) 。請將你的結果連同說明在 12 月 21 日 23:59:59 前放上你的個人網頁。