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EMBOSS GUI PowerPoint Presentation

EMBOSS GUI

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EMBOSS GUI

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

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

  6. Find programs by keywords

  7. Find programs by keywords

  8. html

  9. Displays a program's help documentation manual

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

  11. 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

  12. Restriction Enzyme MAP REMAP

  13. Restriction cutting sites translation

  14. Enzyme cutting frequency

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

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

  17. Plot potential open reading frames PLOTORF

  18. PLOTORF Plot potential open reading frames

  19. GEECEE Calculates fractional GC content of nucleic acid sequences

  20. GEECEE Calculates fractional GC content of nucleic acid sequences

  21. 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

  22. Global alignment NEEDLE Sequence 1 Sequence 2

  23. NEEDLE Global alignment

  24. Local alignment WATER Sequence 1 Sequence 2

  25. Local alignment WATER

  26. Multiple sequence alignment EMMA

  27. Multiple sequence alignment EMMA copy

  28. Displays a multiple sequence alignment SHOWALIGN

  29. Displays a multiple sequence alignment SHOWALIGN Identical sequence

  30. Displays aligned sequences, with colouring and boxing PRETTYPLOT

  31. PRETTYPLOT Displays aligned sequences, with colouring and boxing • PRETTYPLOT

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

  33. http://www.ensembl.org/info/website/archives/index.html

  34. ENSMUSG00000057967

  35. Select Ensembl database

  36. Scans DNA sequences for transcription factors TFSCAN

  37. TFSCAN Scans DNA sequences for transcription factors

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