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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

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