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Bioinformatic Links

 University of Louisville
KBRIN
UofL Bioinformatics Research    Group
CECS Department
Automated Primer Design (local)
Find Gene Names (local)
Feature Annotation Links (local)
Web Blast

 UofL Libraries
Main Library
Kersey Library
Kornhauser Library

 Bioinformatic Courses
University of Louisville 
CECS 694 -- Intro to Bioinformatics

University of Kentucky
Bioinformatics

 
 Databases
NCBI 
EMBL
DDBJ
ensembl
UCSC goldenpath

FlyBase
Rat Genome Database
Mouse Genome Informatics   (MGI)
TIGR
ACeDB
WormBase
AllGenes

SWISS-PROT
BLOCKS
InterPro
Pfam
PRINTS   
PROSITE
 
Clusters of Orthologous Groups   (COGS)
PDB
SCOP  

TRANSFAC
REBASE
Tree of Life

Stanford Microarray Database

January, 2002 NAR Database Issue


 Database Searching
NCBI Blast   
WU Blast  
BLAT (UCSC)

 Sequence Alignment

Sim4
Clustal
ClustalW
MSA
PiP Maker
Sequence Logos

MULTALIN
PIMA
SAM
HMMER
DNA Dot plots

 Phylogeny
Phylip -- J. Felsenstein, UW
PAUP
Joe Felsenstein's Phylogeny Links
ClustalW
TreeView

 Sequence Assembly
GigAssembler -- J. Kent, UCSC
ARACHNE
Phrap
TIGR Assembler
CAP3
 Micro Array Analysis
Microarray Links

 Motif Sampling
Gibbs Sampler -- C. Lawrence,    RPI
MEME
METAMEME
MACAW 

 RNA Secondary Structure
mFOLD
FOLDALIGN		 dynalign
COVE

 Repetitive Elements
RepeatMasker    
MaskerAid   
DUST   		 SEG   
XNU   
RepBase 

 Gene Prediction
Genie      
Twinscan
HMM Gene     		Grail
GenScan
GeneWise

 Commercial Products
Informax
   (Vector NTI, Expression NTI)
GCG
Staden Package
DNA Star  

 Sequencing Centers
Baylor College of Medicine   
Stanford Human Genome   Center
DOE Joint Genome Institute
Washington University GSC
Whitehead Institute MIT
Sanger Centre      

 Miscellaneous

Primer Design
  Primer3

Protein Folding
  PHD
  SSPred
  Stride     

Bioinformatics and Database Searching - PowerPoint Presentation (allow extra time for download)

 

 

 

 

 
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