RESEARCH LINKS
Databases
Blast Search
Saccharomyces Genome Database
MIPS CYGD
Yeast Deletion Project and Proteomics of Mitochondria Database
Mitochondrial Proteome (MitoP2)

Literature Searches    
Eccles Library Catalog
Eccles e-journals
Library of Congress
Marriott Library Catalog
Marriott e-journals
PubMed
NCBI

Funding    
Grantsnet (HHMI, AAAS)
Office of Sponsored Projects
Funding Opportunities

Journals    
Cell
Current Biology
EMBO Journal
Genetics
Journal of Biological Chemistry
Journal of Cell Biology
Molecular Biology of the Cell
Nature
PloS
PNAS
Science
TiBS
TiCB
Traffic

Societies    
American Association for the Advancement of Science
American Society for Biochemistry and Molecular Biology
American Society for Cell Biology
FASEB
National Academy of Science

UNIVERSITY LINKS
Seminars    
Biosciences Calendar
Biochemistry Departmental Seminars
Journal Club RIP
School of Medicine Seminar Series

University of Utah    
University of Utah Homepage
Core Facilities
Department of Biochemistry
Huntsman Cancer Institute
University of Utah Brain Institute

Graduate Programs    
Biological Chemistry
Molecular Biology
Neuroscience

MOLECULAR BIOLOGY LINKS
(Compiled by the Hill Lab)

Sequences/Alignments/Comparisons    
National Center for Biotechnology Information
EMMBOSS a suite of bioinformatics tools.
CLUSTALW
ESPript - color alignments with secondary structure (easy to advanced)
Quick DNA->Protein translation
SMART Simple Modular Architecture Research Tool
pBLAST nBLAST PSI-BLAST or align 2 seqs
BLAST specific genomes:[Human][Mouse][Eukaryotic genomes] [Structural Genomics Target DB]
FFAS Fold and Function assignment server - can gnerate profile and search database with it
pftools ISREC Bioinformatics, profile searching
HMMER (also installed locally) (A tutorial)
Wise2 (Algorithums for DNA searching)
Meta-meme HMM DNA searching

Domain Prediction    
Expasy
SPROT @ EXPASY
Precompiled Alignments of Pfam domain families
Pfam home at HHMI's Janelia Farm
PRODOM - site of micro-domains based on alignments
CDART (NCBI box domains with link to pfam domain number and alignments)
CDD (Conserved Domain Database @ NCBI, standard output of blast with links to domains identified)
DomPred Domain prediction.
Meta-DP Meta-server for domain prediction.
DomPro Domain Prediction
DISOPRED - Disorder Prediction Server
PONDR - Predictor of Natural Disorder Regions
SSEP - Protein Domain Prediction Server

Secondary Structure Prediction and Modeling    
Expasy
Predict Protein (meta Server)
SAM Applications (Sequence Alignment and Modeling)
Swiss-Model
Threader
Robetta (Full chain predictions)
PEPstr - peptide structure prediction (up to 75 residues)
Helical Wheel mapping
PSIPRED - simple predcition - output can be funneled into ESPript.

Primer design    
Primer X Online Quickchange Primer Design
Oligo Calculator
Ambion oligo Calculator
E.coli Genetic Code
E.coli (K12) codon usage table
Protocols - from Cold Spring Harbor
Primer Design tool - Argonne High Throughput
PCR techniques chapter
Ensemble
Primer 3
Net primer

Oligo Synthesis and Sequencing    
Oligo Synthesis Core
Sequencing Core, [results retrieval]

Freeware    
pDRAW

Miscellaneous    

Expasy - Proteomics and bioinformatics portal
Scansite - Protein phosphorylation site prediction
          engine from Michael Yaffe lab
Biology workbench - A master resource of DNA protein
          analysis, cloning etc...
Addgene - A non-profit plasmid repository and
          distribution service