fungene.cme.msu.edu
Functional Gene Pipeline / RepositoryFunctional Gene Pipeline / Repository at Michigan State University
http://fungene.cme.msu.edu/
Functional Gene Pipeline / Repository at Michigan State University
http://fungene.cme.msu.edu/
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Functional Gene Pipeline / Repository | fungene.cme.msu.edu Reviews
https://fungene.cme.msu.edu
Functional Gene Pipeline / Repository at Michigan State University
fungene.cme.msu.edu
Functional Gene Pipeline / Repository
http://fungene.cme.msu.edu/hmm_detail.spr?hmm_id=542
1 - 1000 of 32237 Sequences. Selected sequences : Model Length 283. New to this release. Enterobacter hormaechei subsp. steigerwaltii. Klebsiella pneumoniae subsp. pneumoniae. Klebsiella pneumoniae subsp. ozaenae. Da Fonseca,E.L. Klebsiella pneumoniae subsp. pneumoniae. Extended spectrum beta-lactamase GES-5. Klebsiella pneumoniae subsp. pneumoniae. Da Fonseca,E.L. Carbapenem-hydrolyzing extended-spectrum beta lactamase GES-16. Extended spectrum beta-lactamase GES-1. Da Fonseca,E.L. Silva,V.V. Jr. Klebsi...
Functional Gene Pipeline / Repository
http://fungene.cme.msu.edu/hmm_detail.spr?hmm_id=541
1 - 1000 of 24578 Sequences. Selected sequences : Model Length 381. New to this release. Class C beta lactamase AZECL-57. Enterobacter sp. K66-74. Enterobacter cloacae UCI 49. Enterobacter hormaechei subsp. steigerwaltii. Enterobacter hormaechei subsp. steigerwaltii. Beta-lactamase class C and other penicillin binding proteins. Enterobacter hormaechei subsp. steigerwaltii. Enterobacter hormaechei subsp. steigerwaltii. Enterobacter hormaechei subsp. steigerwaltii. Enterobacter sp. MGH 1. Enterobacter horm...
Functional Gene Pipeline / Repository
http://fungene.cme.msu.edu/tutorial/tutorials.jsp
Button to return to FGPR Home. Functional Gene Pipeline / Repository Tutorials. Short video tutorials demonstrate some of the basic features of the Functional Gene Pipeline. These tutorials average three minutes in length. They capture the screen as the tasks are performed while the narrator explains the tasks and the choices available to the user. (Video portion shows the original tan/green version of our headers; however, tool content and procedures are still accurate.). In the lower right side.
Functional Gene Pipeline / Repository
http://fungene.cme.msu.edu/index.spr;jsessionid=3A72F1229C03946466961A26374EEB08.neptune
If you use RDP's FunGene,. Please cite our most recent article. Begin with these gene links:. Version 8.6 - GenBank 214 (as of 6/22/2016). Process your own Functional Gene data using our new. 8212; Syed Hashsham. 8212; Syed Hashsham. 8212; Robert Stedtfeld. 8212; Robert Stedtfeld. 8212; Robert Stedtfeld. 8212; Robert Stedtfeld. 8212; Robert Stedtfeld. 8212; Syed Hashsham. 8212; Robert Stedtfeld. 8212; Robert Stedtfeld. 8212; Syed Hashsham. 8212; Tamara Tsoi Cole. 8212; Tamara Tsoi Cole. 8212; Tim Johnson.
Functional Gene Pipeline / Repository
http://fungene.cme.msu.edu/FunGenePipeline
Over tool menu item for a popup description;. On the tool menu item to begin working with it. PIPELINE → Pipeline. Run a set of sequences through our standard processing pipeline. Rarr; Pipeline Initial Process. Use the RDP Pipeline to process sequence libraries from raw sequencer output to analysis. DEFINED COMMUNITY ANALYSIS → Defined Community Analysis. Perform error analysis of a defined community. DEREPLICATOR → Dereplicator. USEARCH CHIMERA CHECK → Chimera Check. FRAMEBOT → Framebot. Calculate Shan...
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5
myRDP Login
https://pyro.cme.msu.edu/merger/form.spr;jsessionid=C8070A89438BEB3C085D1F075AB7C955.perry
Your personalized work space. Note about Privacy and Data:. We intend to keep your data private, but your data may be subject to public disclosure due to security issues, programming error, human error, or other reasons. Please keep an up-to-date offline backup of your data at all times. To browse the pipeline tools as a guest please enter the username rdpdemo@demo.edu and password demo. Id (email, lowercase). But data will be erased regularly. 1992-2013 Michigan State University.
myRDP Login
https://pyro.cme.msu.edu/aligner/form.spr;jsessionid=C8070A89438BEB3C085D1F075AB7C955.perry
Your personalized work space. Note about Privacy and Data:. We intend to keep your data private, but your data may be subject to public disclosure due to security issues, programming error, human error, or other reasons. Please keep an up-to-date offline backup of your data at all times. To browse the pipeline tools as a guest please enter the username rdpdemo@demo.edu and password demo. Id (email, lowercase). But data will be erased regularly. 1992-2013 Michigan State University.
myRDP Login
https://pyro.cme.msu.edu/classifier/form.spr;jsessionid=C8070A89438BEB3C085D1F075AB7C955.perry
Your personalized work space. Note about Privacy and Data:. We intend to keep your data private, but your data may be subject to public disclosure due to security issues, programming error, human error, or other reasons. Please keep an up-to-date offline backup of your data at all times. To browse the pipeline tools as a guest please enter the username rdpdemo@demo.edu and password demo. Id (email, lowercase). But data will be erased regularly. 1992-2013 Michigan State University.
Tree Builder - Start
http://rdp.cme.msu.edu/treebuilder/treeing.spr
Tree Builder - Start. Your seq cart contains 0 aligned sequences:. Select sequences for treeing using the Hierarchy Browser. Minimum comparable position is 200. This task will take between 6 seconds and 45 minutes depending on how many sequences were selected and server load (During peroids of extremely high server load, you may not be able to submit requests). 1992-2014 Michigan State University Board of Trustees, East Lansing MI 48824. MSU is an affirmative-action, equal-opportunity employer.
Related Sites
http://rdp.cme.msu.edu/misc/related.jsp
Provides an updated database of gene homologs based on HMM/HMMER search of the GenBank nr database and includes both protein and DNA alignments. Integrated tools are provided for primer testing, phylogenetic analysis and model refinement. A comprehensive database containing published rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information. probeBase. Can be searched for target organisms or probe names and is maintained by the Microbial Ecology Group. The Integrate...
Sequence Match
http://rdp.cme.msu.edu/seqmatch/seqmatch_intro.jsp
You can select sequences from. And Hierarchy Browser to do seqmatch? Percent identity scores will be reported for aligned sequences (limited to 2000). Please enter your sequences:. Choose a file to upload. Cut and paste sequence(s) (in Fasta, GenBank, or EMBL format):. Note: Javascript must be enabled on your browser to use this RDP tool. Type strain information is provided by bacterial taxonomy. View only near-full-length sequences (. 1200 bases), short partials, or both.
Classifier
http://rdp.cme.msu.edu/classifier/classifier.jsp
NEW procedural tutorials for CLASSIFIER. Classifier now provides gene copy number adjustment. For 16S gene sequences. The 16S gene copy number data is provided by rrnDB. For detailed analysis. The Warcup V2 release notes. Is released in June 2016. How to cite Classifier? The RDP Classifier publication has been selected by Essential Science Indicators as the most-cited paper in a highlighted research area of microbiology. It's featured in December 2011 Science Watch. Please enter your sequences:. MSU is a...
RDP Tutorial
http://rdp.cme.msu.edu/help/tutorial.jsp
RDP has released NEW PROCEDURAL TUTORIALS. That take you through the basic steps of a web-based sequence analysis workflow with sample and test files. There are also links individual command-line tool instructions to aid in getting sequences ready for further processing. Please give them a try and offer any comments or suggestions for improvement. Begin tutorials here: http:/ rdp.cme.msu.edu/tutorials/RDPtutorial CONTENTS.html. Using RDPTools Output with R/Bioconductor package Phyloseq.
RDP Release Notes
http://rdp.cme.msu.edu/misc/rel10info.jsp
Ribosomal Database Project Release 11. Please note the RDP License Agreement and how to cite services from this site. RDP Release 11 Notes. Notes and Clarifications About RDP. Release 11 Update History. RDP Release 11 Notes. RDP Release 11 provides many significant enhancements over RDP release 10:. New Data Collection- Fungal 28S rRNA Sequences. New and Updated Alignment. This aligner has several advantages: it incorporates secondary-structure information into the alignment process; as a model-based ali...
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Functional Gene Pipeline / Repository
If you use RDP's FunGene,. Please cite our most recent article. Begin with these gene links:. Version 9.5 - GenBank 223 (as of 2/16/2018). Process your own Functional Gene data using our new. 8212; Syed Hashsham. 8212; Syed Hashsham. 8212; Robert Stedtfeld. 8212; Robert Stedtfeld. 8212; Robert Stedtfeld. 8212; Robert Stedtfeld. 8212; Robert Stedtfeld. 8212; Syed Hashsham. 8212; Robert Stedtfeld. 8212; Robert Stedtfeld. 8212; Syed Hashsham. 8212; Tamara Tsoi Cole. 8212; Tamara Tsoi Cole. 8212; Xun Qian.
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