Primary Links
NCBI Entrez
NCBI Map Viewer
TIGR
Pfam
GeneScan
FGENESH
EMBL
KEGG
Cholera
Genome (Vibrio cholerae)
SGD (Saccharomyces cervisceae)
Wormbase
(Caenorhabditis
elegans)
FlyBase (Drosophila melanogaster)
TAIR (Arabidopsis thaliana)
MGI (Mus musculus)
Plasmid Genome Database
Other Links and
Tools
GNN - Genome News
Network
GeneMark
for Prokaryotes
ClustalW at EMBL
BoxShade
Cn3D
tutorial at NCBI
PSI-BLAST tutorial at NCBI
Glimmer3
PDB
Molecules2Go
ExPASy
tRNAscan-SE
TRANSFAC
TopPred
PSORT
TargetP
JDotter
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Exercises
E1. Exploring
sequence databases (Ex1.html)
E2. Repetitive
DNA (Ex2.html)
E3. Finding
genes (Ex3.html)
E4. E-vaues (Ex4.doc)
E5. BLAST
(Ex5.html)
E6. Multiple
Alignments (Ex6.html)
E7. Introduction
to Artemis (Ex7.html)
E8. Introduction
to Sequencher (Ex8.html)
E9. Restriction Digests (Ex9.html)
E10. Bioinformatics (Ex10.html)
E11. Mozy Initial Sequence Analysis (Ex11.html)
E12. Mozy Genome Annotation (Ex12.html)
E13. Mozy Genome Annotation Continued (Ex13.html)
E14. Dynamic Programming (Ex14.html)
E15. Designing Primers (Ex15.html)
Lab
Files
Photos
from the field trip
Gene Family Project
Venter Video
Mozy contig map
Ubuntu
PPT
Files from Lecture
P1. Lab Overview.ppt
P2. Molecular Biology review.ppt
P3. Blue/white screening and sequencing
P4. Gene finding/Srr-2
P5. Matrix and Gene families
P6. Pathways
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PDF Files
Midterm paper (HIV-1.pdf)
Horizontal gene flow.pdf
Bordetella Genomes.pdf
Bioinformatics software.pdf
Markov.pdf
History
of Genomics.pdf
GenBank.pdf
Human genome paper
Gene
structure prediction.pdf
Dynamic programming.pdf
BLAST.pdf
Glycolytic enzymes.pdf
Ascorbate peroxidase.pdf
Placental.pdf
Elephants.pdf
Pfam.pdf
Poliovirus.pdf
Branched-chain amino acid.pdf
Sargasso Sea.pdf
Giles.pdf
Sequence Files
Sample ClustalW nt data
Sample ClustalW aa data
Mozy contigs
Reordered, assembled Mozy contigs
Reordered Mozy contigs
Mozy annotation.tab
Mozy PCR primers
Mozy annotation (version 2).tab
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