Introduction to the GCG Wisconsin Package

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Transcript 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: [email protected]
Fax: (919)843-3103
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.
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.
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.
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.
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.
Databases GCG Supports
 Nucleic
acid databases
 GenBank
 EMBL
 Protein
(abridged)
databases
 NRL_3D
 UniProt
(SWISS-PROT, PIR, TrEMBL)
 PROSITE, Pfam,
Restriction
Enzymes (REBASE)
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.
File Importing and Exporting
 Reformat
 FromEMBL
 FromGenBank
 FromPIR
 FromStaden
 FromIG
 FromFastA
ToPIR
ToStaden
ToIG
ToFastA
File Formats with GCG
 Single
sequence files (in GCG format)
 List (a list of files)
 MSF (multiple sequence format)
 RSF (rich sequence format)
Typical program
Result from MAP analysis
X-Windows server must be running
SeqLab Main Window (List Mode)
SeqLab Editor Mode
Display by Features
SeqLab Editor Mode (cont.)
SeqLab Output Manager
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
Create your own sequence
PlasmidMap
FindPatterns
HmmerPfam Analysis
Gene Finding (FRAME)
Restriction Enzyme Map
Consensus Sequence
Phylogenetic Tree (Cladogram)
Peptide Structure
Peptide Structure (2)
Isoelectric Analysis
Transmemberane Domains
Neucleic Acid 2nd Structure
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.
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.
Comparison of two sequences
GapShow
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.
Multiple Comparison by Pileup
Multiple Comparison by Pileup
Dendrogram by Pileup
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.
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.
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.
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.
Profile Hidden Markov Model
HmmerSearch
HmmerSearch (cont.)
HmmerSearch (cont.)
HS (cont.Histogram of scores)
HS (cont. resulting alignment)
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.
NetBLAST
PSIBLAST
 Similar
to BLAST, except using positionspecific scoring matrices during the
search.
 Use protein sequence(s) to iteratively
search protein database(s).
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.
MEME PROFILE
MEME (cont.)
GrowTree (Cladogram)
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).
Sign up BioScience
Log onto GCG
Log onto GCG (cont.)
GCG Welcome Page
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
DISPLAY=yourMachineIP:0.0;
 Enter the command “xterm &” to activate the
xterm window;
 On the GCG main window enter the
command “seqlab &” to activate the SeqLab
GUI.
How to get SeqLab to run
(cont.)