Other Resources
Database Sequence Tools | General Bioinformatic Tools | Program Script Editors | Sequence Data | UD Resources
Database Sequence Tools:
- DOE Greengenes:
http://greengenes.lbl.gov/cgi-bin/nph-index.cgi - DOE Human Genome Map:
http://tinyurl.com/b24f9j - DOE Integrated Microbial Genomes system:
http://img.jgi.doe.gov/cgi-bin/pub/main.cgi - Center for Biological Sequence Analysis, Technical University of Denmark:
http://www.cbs.dtu.dk/biotools/ - European Bioinformatics Institute:
http://www.ebi.ac.uk/Tools/ - GenBank Microbial Genomes:
(web)http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi
(ftp) ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ - rRNA Pyrosequencing Analysis and Databases
Ribosomal Database Project Pyrosequencing Pipeline:
http://pyro.cme.msu.edu/pyro/index.jsp - US National Center for Biotechnology Information:
http://www.ncbi.nlm.nih.gov/Tools/ - Visualization and Analysis of Microbial Population Structures:
http://vamps.mbl.edu/resources/databases.php - CAMERA - Community Cyberinfrastructure for Advanced Marine Microbial
Ecology Research and Analysis:
http://camera.calit2.net/index.php - RAST - Rapid Annotation using Subsystem Technology:
http://rast.nmpdr.org - MG/RAST Meat Genome Rapid Annotation using Subsystem Technology:
http://metagenomics.nmpdr.org
General Bioinformatic Tools:
- Python:
http://www.python.org - R:
http://www.r-project.org - BioPython:
http://biopython.org/wiki/Main_Page Python - Plotting matplotlib:
http://matplotlib.sourceforge.net/ - Scientific Python (NumPy):
http://www.scipy.org/ - The Scriptome-Protocols for Manipulating Biological Data
http://sysbio.harvard.edu/CSB/resources/computational/scriptome/
Sequence Data:
- Environmental Sequences from Toolik Lake , LTER; Campbell et al., "The effect of nutrient deposition on bacterial communities in Arctic tundra soil", Environmental Microbiology.
(File 1) http://www.ceoe.udel.edu/CEG/resources/tlallgroups.zip
(File 2) http://www.ceoe.udel.edu/CEG/resources/tlallfasta.zip
- 16S rRNA tag sequence data from the Arctic Ocean, Kirchman et al. "The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes". Environ. Microb. In press.
(File 1) http://www.ceoe.udel.edu/CEG/resources/ArcticTagData.zip
UD Resources:
- UD Biowolf Computing Cluster:
http://bioit.dbi.udel.edu/howto/sge - Bioinformatics Program at UD:
http://bioinformatics.udel.edu - Beginning Bioinformatics:
http://icewater.cms.udel.edu/IntroPerl/ - Environmental Bioinformatics:
http://icewater.cms.udel.edu/EnvBioInfo/
