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Introduction to the GCG Wisconsin Package

Introduction to the GCG Wisconsin Package. The Center for Bioinformatics UNC at Chapel Hill Jianping (JP) Jin Ph.D. Bioinformatics Scientist Phone: (919)843-6105 E-mail: jjin@email.unc.edu Fax: (919)843-3103. What is GCG.

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Introduction to the GCG Wisconsin Package

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  1. Introduction to the GCG Wisconsin Package The Center for Bioinformatics UNC at Chapel Hill Jianping (JP) Jin Ph.D. Bioinformatics Scientist Phone: (919)843-6105 E-mail: jjin@email.unc.edu Fax: (919)843-3103

  2. What is GCG • An integrated package of over 130 programs (the GCG Wisconsin Package). • For extensive analyses of nucleic acid and protein sequences. • Associated with most major public nucleic acid and protein databases. • Works on UNIX OS.

  3. Why use GCG • Removes the need for the constant collection of new software by end users. • Removes the need to learn new interface as new software is released. • Provides a flow of analyses within a single interface. • Unix environment allows users to automate complex, repetitive tasks. • Allows users to use multiple processors to accelerate their jobs. • Supports almost all public databases that can be updated daily. Fast local search.

  4. Flexibility or Automation • 1. MEME: upstream regulatory motifs; • 2. MotifSearch: genes sharing these potential regulatory motifs; • 3. PileUp: multiple sequence alignment; • 4. Distances: extract pairwise distances from the alignment; • 5. GrowTree: a phylogenetics tree.

  5. Interfaces • Command Line: Running programs from UNIX system prompt. • SeqLab: Graphic User’s Interface, requiring an X windows display. • SeqWeb: to a core set of sequence analysis program.

  6. Limitations with GCG • The GUI interface does not give the users the full access to the power of the command line, nor to the complete set of programs. • Many programs place a limit of the maximum size of the sequences that they can handle (350 Kb). This limitation will be removed in version 11.

  7. Databases GCG Supports • Nucleic acid databases • GenBank • EMBL (abridged) • Protein databases • NRL_3D • UniProt (SWISS-PROT, PIR, TrEMBL) • PROSITE, Pfam, • Restriction Enzymes (REBASE)

  8. Database Update Services • DataServe: Automatically updates nucleic acid on a daily basis via FTP. • DataExtended: the most compete set of nucleic acid and protein data. The timing of the release is coordinated with the major GenBank release, 2-3 months. • DataBasic: Similar to DataExtended, but excludes EST and GSS data from GenBank and EMBL.

  9. File Importing and Exporting • Reformat • FromEMBL • FromGenBank • FromPIR ToPIR • FromStaden ToStaden • FromIG ToIG • FromFastA ToFastA

  10. File Formats with GCG • Single sequence files (in GCG format) • List (a list of files) • MSF (multiple sequence format) • RSF (rich sequence format)

  11. Typical program

  12. Result from MAP analysis

  13. X-Windows server must be running

  14. SeqLab Main Window (List Mode)

  15. SeqLab Editor Mode

  16. Display by Features

  17. SeqLab Editor Mode (cont.)

  18. SeqLab Output Manager

  19. GCG Programs • 1. Comparison • 2. Database Searching and Retrieval • 3. DNA/RNA Secondary Structure • 4. Editing and Publication • 5. Evolution • 6. Fragment Assembly • 7. Importing and exporting • 8. Mapping • 9. Primer Selection • 10. Protein Analysis • 11. Translation

  20. Create your own sequence

  21. PlasmidMap

  22. FindPatterns

  23. HmmerPfam Analysis

  24. Gene Finding (FRAME)

  25. Restriction Enzyme Map

  26. Consensus Sequence

  27. Phylogenetic Tree (Cladogram)

  28. Peptide Structure

  29. Peptide Structure (2)

  30. Isoelectric Analysis

  31. Transmemberane Domains

  32. Neucleic Acid 2nd Structure

  33. Pairwise Comparison (Gap) • Neelman & Wunsch algorithm. • A global alignment covering the whole length of both sequences and the resulting sequences are of the same length with inserted gaps. • Good when two sequences are closely related.

  34. Pairwise Comparison (BestFit) • Algorithm of Smith and Waterman. • Local homology alignment that finds the best segment of similarity b/w two sequences. • The most sensitive sequence comparison method available.

  35. Comparison of two sequences

  36. GapShow

  37. Multiple Comparison (PileUp) • The method of Feng and Doolittle similar to Higgins & Sharp. • A series of progressive pairwise alignments (up to 500 seq.) generate a final alignment. • An extension of Gap, not ideal for finding the best local region of similarity, such as a shared motif.

  38. Multiple Comparison by Pileup

  39. Multiple Comparison by Pileup

  40. Dendrogram by Pileup

  41. Database Search • Nearly always employ local alignment algorithms. • Often use “heuristic” methods (for a screen), FASTA and BLAST. • Assures the seq.are given correct local similarity score, but no guarantee that all seq. with high Smith-Waterman scores pass through the screen.

  42. BLAST • Accepts a number of sequences as input and specify any number of DBs. $Blast –INfile2=PIR,SWPLUS; -INfile=hsp70.msf{*}. • Support 5 BLAST programs, but no gap alignment available for TBLASTX. • For non-coding nucleotide homology search, considering either reducing the word size from 11 to 6/7, or using the FASTA. • The number of scoring matrices is limited, BLOSUM62/45/80 and PAM70 available for –MATRix parameter.

  43. Database Search (SSearch) • A rigorous Smith-Waterman search for similarity between a query sequence and a group of sequences of the same type. • The most sensitive method available for similarity search. • Very slow.

  44. HmmerSearch • Use a profile HMM as a query to search a sequence database. • Profile HMM: a position specific scoring table, a statistical model of the consensus of a multiple sequence alignment. • Output can be used for any GCG program that accepts list file.

  45. Profile Hidden Markov Model

  46. HmmerSearch

  47. HmmerSearch (cont.)

  48. HmmerSearch (cont.)

  49. HS (cont.Histogram of scores)

  50. HS (cont. resulting alignment)

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