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HMMER (pfam)

Downloaded from the website. Compiled using:

env CFLAGS="-O3" ./configure --enable-threads --enable-lfs
-fast wasn't any better (seems to be for G5 only)

Had to drag and drop binaries to /usr/local/bin

 

Fink

Download and install fink as usual. Did install the latest X11 for Leopard linked from fink site.

install:
arb
bioperl
biopython
 
biopython has clustalw as a dependency. To get arb and clustalw to play nice, edit:
sw/fink/dists/unstable/main/finkinfo/sci/arb.info
and remove apropriate packages from "Conflicts:" line.
Then install final conflicting package with something like:
sudo dpkg --force-overwrite -i arb_20071207-1005_darwin-i386.deb

 

To get arb pt_server working:
ln -s /sw/bin /sw/share/arb/bin

edit /etc/hosts.
Change:
127.0.0.1    localhost
to
127.0.0.1    localhost    rocapws.ocean.washington.edu

Mac Pro

Setup the new mac pro.

GenomeDiagram

GenomeDiagram, Pretty much as described on webpages, but need to to libjpeg and freetype with fink. Several prerequesites, but straight forward.

REPK

Restriction Enzyme Picker Online, v.1.2

by Gabrielle Rocap and Eric Collins (rec3141.at.gmail.com)

REPK (Restriction Endonuclease Picker) finds sets of 4 commercially available restriction endonucleases which together uniquely differentiate designated sequence groups from a supplied FASTA format sequence file for use in T-RFLP. If you have a database of known sequences from an environment, this program could be useful to pick some enzymes that uniquely discriminate the different groups in your database.

Read the Manual

Enter your FASTA aligned sequences here:
(Here is an example input file: alignment5.txt)

Select the enzymes you would like to use: (REBASE Version 807)
(Hold down the [Control] key to deselect, or to select multiple enzymes)

Type IIA enzymes (forward and reverse [+])

Enter any custom enzymes you would like to use in the following format (where ^ is the cut site):
NoCut zzz^zzz

Taxonomic rank: : which taxonomic group do you want separated out?
CHECK TAXONOMIC RANKS INSTEAD OF RUNNING REPK

Cutoff: : furthest apart two fragments can be in length and still be considered the same fragments

Min Fragment Lengths: : shortest acceptable fragment (must be greater than Cutoff)

Max Fragment Lengths: : longest acceptable fragment

Stringency: : an enzyme must distinguish MORE than this percent of groups to be acceptable

Max Missing Group Combinations: : the number of missing groups allowed

Max Matches Returned: : the most number of matches to print out (maximum 1000)



OPTIONAL -- Enter your RDP Classifier output file here -- OPTIONAL
(Here is an example input file: rdpdownload5.txt or generate your own here: RDP-Classifier)



CITE REPK
If you find REPK useful in your research please cite:

Collins, R. E. and G. Rocap. 2007. REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis. Nucleic Acids Res. 35 (Database issue): W58-W62; doi:10.1093/nar/gkm384 [Free full text]

Source code, help, and license information is available via Google Code:
http://code.google.com/p/repk

Please report bugs or other problems here:
http://code.google.com/p/repk/issues/list

Version Changes
1.2 -- Added Visual Enzyme Match Matrix
1.1 -- Added Taxonomic Rank Checker
1.0 -- Initial Release

 

NSF logo

Support for the development of REPK provided by the National Science Foundation under Grant No. OPP-0327244 to J.W. Deming and OCE-0822026 and OCE-0352190 to G. Rocap, as well as a Washington Sea Grant award to J.W. Deming.

Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF)

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Tools

The purpose of this section of the site is to provide tools for interested parties to use some of the tools we have developed for our research.

Publications

Ahlgren, N. A. and G. Rocap. 2006. Culture isolation and culture-independent clone libraries reveal new marine Synechococcus ecotypes with distinctive light and N physiologies. Applied and Environmental Microbiology 72: 7193-7204. PDF file (752 kb)

Fuchsman, C. A. and G. Rocap. 2006. Whole genome reciprocal BLAST analysis reveals Planctomycetes do not share an unusually high number of genes with Eukarya and Archaea. Applied and Environmental Microbiology 72:6841-6844 PDF file (214 kb)

Van Mooy, B.A.S., G. Rocap, H. F. Fredricks, C. T. Evans and A. H. Devol. 2006. Sulfolipids dramatically decrease phosphorus demand by picocyanobacteria in oligotrophic marine environments. PNAS. 103:8607-8612. PDF file (856 kb)

Ahlgren, N. A., G. Rocap, and S. W. Chisholm. 2005. Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies Environmental Microbiology 8: 441-454 PDF file (257 kb)

Saito, M. A., G. Rocap, and J. W. Moffett. 2005. Production of Cobalt Binding Ligands in a Synechococcus Feature at the Costa Rica Upwelling Dome. Limnology and Oceanography 50: 279-290. PDF file (380 kb)

Rocap, G., F. W. Larimer, J. Lamerdin, S. Malfatti, P. Chain, N. A. Ahlgren, A. Arellano, M. Coleman, L. Hauser, W. R. Hess, Z. I. Johnson, M. Land, D. Lindell, A. F. Post, W. Regala, M. Shah, S. L. Shaw, C. Steglich, M. B. Sullivan, C. S. Ting, A. Tolonen, E. A. Webb, E. R. Zinser and S. W. Chisholm. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047. PDF file (430 kb)
Supplementary Information (418 kb)

Rocap, G., D. L. Distel, J. B.Waterbury and S. W. Chisholm. 2002. Resolution of Prochlorococcus and Synechococcus ecotypes using 16S-23S rRNA internal transcribed spacer (ITS) region sequences. Applied and Environmental Microbiology, 68: 1180-1191. PDF file (362 kb)

Ting, C. S., G. Rocap, J. King and S. W. Chisholm. 2002. Cyanobacterial Photosynthesis in the Oceans: Origins and Significance of Divergent Light Harvesting Strategies. Trends in Microbiology. 10:134-142. PDF file (136 kb)

Moore, L. R., A. F. Post, G. Rocap and S. W. Chisholm. 2002. Differential nitrogen utilization of the marine cyanobacteria Prochlorococcus and Synechococcus. Limnology and Oceanography 47: 989-996. PDF file (178 kb).

Hess, W. R., G. Rocap, C. S. Ting, F. W. Larimer, S. Stilwagon, J. Lamerdin and S. W. Chisholm. 2001. The photosynthetic apparatus of Prochlorococcus - a genomic perspective. Photosynthesis Research, 70:53-71. PDF file (717 kb)

Ting, C., G. Rocap, J. King and S. W. Chisholm. 2001. Phycobiliprotein genes of the marine prokaryote Prochlorococcus: Evidence for rapid evolution of genetic heterogeneity. Microbiology 147: 3171-3182. PDF file (1.6 Mb)

Rocap, G., L. R. Moore and S. W. Chisholm. 1999. Molecular Phylogeny of Prochlorococcus ecotypes. in Marine Cyanobacteria, L. Charpy and A. W. D. Larkum ed. Bulletin de líInstitute Océanographique, Monaco, special issue No. 19. pp. 107-116. PDF file (548 kb)

Moore, L. R., G. Rocap and S. W. Chisholm. 1998. Physiology and Molecular Phylogeny of Coexisting Prochlorococcus ecotypes. Nature 393: 464-467. PDF file (345 kb)

Genome enabled ecology of marine microbes

 

The Thompson

Welcome to the home page of the Rocap lab, located in the School of Oceanography at the University of Washington. I am a marine microbial ecologist interested in the evolution and ecology of marine bacteria and phytoplankton. We use a variety of approaches in the lab; physiological (growth experiments and pigment analyses), molecular (quantitative PCR, sequencing and expression assays) and computational (phylogenetic analyses, comparative genomics). The multiple projects in the lab all address common questions: How does genetic diversity arise in marine microbial populations, how is it maintained, and how does it influence ecological success.

Our lab is part of the Marine Molecular Biology Lab, a facility within the College of Ocean and Fishery Sciences at UW. Researchers at MMBL are a diverse group, united by the use of molecular techniques to address ecological questions in aquatic environments.

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