Introduction to the GCG Wisconsin Package

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Introduction to the GCG Wisconsin Package

• The Center for Bioinformatics
• UNC at Chapel Hill
• Jianping (JP) Jin Ph.D.
• Bioinformatics Scientist
• Phone [phone]
• E-mail jjin_at_email.unc.edu
• Fax [phone]

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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.

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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.

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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.

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Interfaces

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

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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.

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Databases GCG Supports

• Nucleic acid databases
• GenBank
• EMBL (abridged)
• Protein databases
• NRL_3D
• UniProt (SWISS-PROT, PIR, TrEMBL)
• PROSITE, Pfam,

• Restriction Enzymes (REBASE)

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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.

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File Importing and Exporting

• Reformat
• FromEMBL
• FromGenBank
• FromPIR ToPIR
• FromStaden ToStaden
• FromIG ToIG
• FromFastA ToFastA

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File Formats with GCG

• Single sequence files (in GCG format)
• List (a list of files)
• MSF (multiple sequence format)
• RSF (rich sequence format)

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Typical program
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Result from MAP analysis
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X-Windows server must be running
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SeqLab Main Window (List Mode)
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SeqLab Editor Mode
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Display by Features
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SeqLab Editor Mode (cont.)
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SeqLab Output Manager
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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

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Create your own sequence
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PlasmidMap
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FindPatterns
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HmmerPfam Analysis
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Gene Finding (FRAME)
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Restriction Enzyme Map
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Consensus Sequence
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Phylogenetic Tree (Cladogram)
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Peptide Structure
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Peptide Structure (2)
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Isoelectric Analysis
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Transmemberane Domains
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Neucleic Acid 2nd Structure
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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.

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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.

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Comparison of two sequences
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GapShow
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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.

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Multiple Comparison by Pileup
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Multiple Comparison by Pileup
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Dendrogram by Pileup
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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.

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BLAST

• Accepts a number of sequences as input and
  specify any number of DBs. Blast
  INfile2PIR,SWPLUS -INfilehsp70.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.

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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.

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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.

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Profile Hidden Markov Model
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HmmerSearch
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HmmerSearch (cont.)
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HmmerSearch (cont.)
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HS (cont.Histogram of scores)
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HS (cont. resulting alignment)
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NetBLAST

• Sends your query sequences over the internet to a
  server at NCBI, Bethesda.
• Some limitations on NetBLAST, e.g. prohibiting
  TBLASTX search vs. the nr database, only Alu,
  EST, GSS, STS.
• Not support as many options as are available
  with BLAST.

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NetBLAST
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PSIBLAST

• Similar to BLAST, except using position-specific
  scoring matrices during the search.
• Use protein sequence(s) to iteratively search
  protein database(s).

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MEME and MotifSearch

• Multiple EM Motif Elicitation, a tool for
  discovering motifs in a group of DNA or protein
  sequences.
• Motif a sequence pattern that occurs repeatedly
  in a group of related sequences.
• Use a set of MEME profiles to search a database
  for new sequences similar to the original family.

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MEME PROFILE
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MEME (cont.)
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GrowTree (Cladogram)
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Access to GCG on Campus

• 1. Onyen and password plus sign up to BioSci
  service at http//onyen.unc.edu
• 2. Computer connected to the Campus network
• 3. Postscript printer connected to the campus
  network
• 4. SSH Secure Client
• 5. X-Windows Server (optional).

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Sign up BioScience
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Log onto GCG
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Log onto GCG (cont.)
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GCG Welcome Page
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How to get seqlab to run

• Open X-Windows
• Logon to the GCG server, nun.isis.unc.edu,
  through SSH Secure Shell Client
• At the prompt () enter the command export
  DISPLAYyourMachineIP0.0
• Enter the command xterm to activate the xterm
  window
• On the GCG main window enter the command seqlab
  to activate the SeqLab GUI.

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How to get SeqLab to run (cont.)