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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
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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
Oligo Synthesis and Sequencing
Oligo Synthesis
Core
Sequencing
Core, [results
retrieval]
Freeware
pDRAW |
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