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TARGeT

TARGeT: Tree Analysis of Related Genes and Transposons. Yujun Han*, James Burnette* , and Susan Wessler*. Center for Human Genome Variation, Duke Univeristy. Department of Botany and Plant Sciences, University of California Riverside Nucleic Acids Research Article. Choose your TARGeT start page:. TARGeT using Approximately-Maximum-likelihood with FastTreeMP. TARGeT using blastn with DNA query. TARGeT using tblastn with Protein query. TARGeT using Neighbor Joining with TreeBest. Browser and the latest Java.

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TARGeT: Tree Analysis of Related Genes and Transposons. Yujun Han*, James Burnette* , and Susan Wessler*. Center for Human Genome Variation, Duke Univeristy. Department of Botany and Plant Sciences, University of California Riverside Nucleic Acids Research Article. Choose your TARGeT start page:. TARGeT using Approximately-Maximum-likelihood with FastTreeMP. TARGeT using blastn with DNA query. TARGeT using tblastn with Protein query. TARGeT using Neighbor Joining with TreeBest. Browser and the latest Java.
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TARGeT | target.iplantcollaborative.org Reviews

https://target.iplantcollaborative.org

TARGeT: Tree Analysis of Related Genes and Transposons. Yujun Han*, James Burnette* , and Susan Wessler*. Center for Human Genome Variation, Duke Univeristy. Department of Botany and Plant Sciences, University of California Riverside Nucleic Acids Research Article. Choose your TARGeT start page:. TARGeT using Approximately-Maximum-likelihood with FastTreeMP. TARGeT using blastn with DNA query. TARGeT using tblastn with Protein query. TARGeT using Neighbor Joining with TreeBest. Browser and the latest Java.

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target.iplantcollaborative.org target.iplantcollaborative.org
1

TARGeT: Tree Analysis of Related Genes, Protein version 3.4

http://target.iplantcollaborative.org/v3.4.1_TATE_protein_start.php

TARGeT: Using Protein Query (tblastn). Choose a Database and enter a Query. Steps of TARGeT and optional settings. You can choose more than one database. Citrus clementina - clementine. Citrus sinensis - sweet orange. Citrus sinensis - CsiDB201301. Citrus sinensis - Csin1.0-14. Cucumis sativus - Cucumber. Glycine max - Soybean. Manihot esculenta - Cassava. Mimulus guttatus - Monkeyflower. Morus notabilis - Mulberry. Oryza sativa japonica - Rice. Oryza sativa japonica Version 7. Vitis vinifera - Grape.

2

TARGeT Nucleotide version 3.4 (ML)

http://target.iplantcollaborative.org/v3.4.1_TATE_dna_start.php

TARGeT: Using a Nucleotide Query (blastn). Choose a Database and enter a Query. Steps of TARGeT and optional settings. You can choose more than one database. Citrus clementina - clementine. Citrus sinensis - sweet orange. Citrus sinensis - CsiDB201301. Citrus sinensis - Csin1.0-14. Cucumis sativus - Cucumber. Glycine max - Soybean. Manihot esculenta - Cassava. Mimulus guttatus - Monkeyflower. Morus notabilis - Mulberry. Oryza sativa japonica - Rice. Oryza sativa japonica Version 7. Vitis vinifera - Grape.

3

TARGeT Nucleotide version 3.3

http://target.iplantcollaborative.org/v3.3_TATE_dna_start.php

TARGeT: Using a Nucleotide Query (blastn). Choose a Database and enter a Query. Steps of TARGeT and optional settings. You can choose more than one database. Citrus clementina - clementine. Citrus sinensis - sweet orange. Citrus sinensis - CsiDB201301. Citrus sinensis - Csin1.0-14. Cucumis sativus - Cucumber. Glycine max - Soybean. Manihot esculenta - Cassava. Mimulus guttatus - Monkeyflower. Morus notabilis - Mulberry. Oryza sativa japonica - Rice. Oryza sativa japonica Version 7. Vitis vinifera - Grape.

4

TARGeT version 3

http://target.iplantcollaborative.org/v3_multiple_align_step1.html

TARGeT: Prepare a Multiple Query Step 1. Copy and paste your query sequences in the box. Only fasta format sequence data is accepted. Each query must have unique name. A multiple alignment will be generated with the query sequences using Muscle.

5

Determine is a DNA sequence is a TE

http://target.iplantcollaborative.org/TE_boundary_start.php

Citrus clementina - clementine. Citrus sinensis - sweet orange. Citrus sinensis - CsiDB201301. Citrus sinensis - Csin1.0-14. Cucumis sativus - Cucumber. Glycine max - Soybean. Manihot esculenta - Cassava. Mimulus guttatus - Monkeyflower. Morus notabilis - Mulberry. Oryza sativa japonica - Rice. Oryza sativa japonica Version 7. Populus trichocarpa - Poplar. Ricinus communis - Castor Bean. Vitis vinifera - Grape. Zea mays - Maize/Corn. Zea mays Palomero unassembled. Acyrthosiphon pisum - Pea Aphid. Solanum...

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genomevolution.org genomevolution.org

System Support - CoGepedia

https://genomevolution.org/wiki/index.php/System_Support

CoGe System Support, 2013. Contact us at coge.genome@gmail.com! CoGe is a comparative genomics system funded by Gordon and Betty Moore Foundation and is provided as a public research toolbox. Use is without charge. CoGe is a collaboration with the Lyons Lab at the University of Arizona, the Freeling Lab at UC Berkeley, and the iPlant Collaborative. NSF has supported CoGe in the past. Additional tools and data are provided by volunteer contributors. Please read our data usage policy. The CoGe team underst...

genomevolution.org genomevolution.org

CoGepedia

https://genomevolution.org/wiki/index.php

Welcome to CoGepedia, CoGe's Official Wiki. Here you can find information pertaining to the CoGe Comparative Genomics suite of web-tools, including:. How to get a CoGe account. How to add a private genome to CoGe. Background on comparative genomics terms and science. What is needed to run CoGe? Funding for CoGe is provided by:. Retrieved from " https:/ genomevolution.org/wiki/index.php? Sites Linked to CoGe. Sites Linked from CoGe. This page was last modified on 16 April 2015, at 12:18.

genomevolution.org genomevolution.org

CoGepedia

https://genomevolution.org/wiki

Welcome to CoGepedia, CoGe's Official Wiki. Here you can find information pertaining to the CoGe Comparative Genomics suite of web-tools, including:. How to get a CoGe account. How to add a private genome to CoGe. Background on comparative genomics terms and science. What is needed to run CoGe? Funding for CoGe is provided by:. Retrieved from " https:/ genomevolution.org/wiki/index.php? Sites Linked to CoGe. Sites Linked from CoGe. This page was last modified on 16 April 2015, at 12:18.

genomevolution.org genomevolution.org

Tutorials - CoGepedia

https://genomevolution.org/wiki/index.php/Tutorials

Here you can find tutorials informing you on how to get the most out of CoGe's tools. How to search and assemble genes. How to assemble contig-level de novo assembly using a reference genome using synteney. How to determine the structural changes between genome assemblies. How to do phylogenetics with CoGe. How to download a genome and its annotations. How to find syntenic regions between genomes. What to do with a genome in the early stages of assembly. How to load genomes into CoGe. How to share genomes.

genomevolution.org genomevolution.org

FAQs - CoGepedia

https://genomevolution.org/wiki/index.php/FAQs

Commonly asked questions about CoGe. Why call it CoGe? Why make another comparative genomics system? How is CoGe designed and put together? What is needed to run CoGe? What is CoGe's sequence analysis workflow or pipeline? What web browser do you recommend and how should it be configured? What programming languages/software are used in CoGe? Can I add a genome? What is CoGe's data release policy? What is CoGe's Graphical Genomic Visualization Library? Can CoGe be installed locally. How can I link to CoGe?

genomevolution.org genomevolution.org

How to get a CoGe account - CoGepedia

https://genomevolution.org/wiki/index.php/How_to_get_a_CoGe_account

How to get a CoGe account. CyVerse's authentication system login page. CoGe is federated with CyVerse's Authentication Service. This means that in order to login to CoGe you need a CyVerse account. Once you log into CoGe, you can:. Load genomes and keep them private. Load experiments (functional and diversity data sets for genomes) and keep them private. Share private genomes and experiments with other users. Have private genomes and experiments shared with you. Track all your previously run analyses.

genomevolution.org genomevolution.org

New to CoGe - CoGepedia

https://genomevolution.org/wiki/index.php/New_to_CoGe

CoGe's dynamic interactive genome browser. Displaying various types of information about the genome of Escherichia coli including codon usage, histogram of CDS. GC content, and amino acid usage. Organism can be viewed at: http:/ synteny.cnr.berkeley.edu/CoGe/OrganismView.pl? Syntenic dotplot by SynMap. Syntenic comparison of two regions from the genome of Arabidopsis thaliana using GEvo. Getting CoGe to run. Get a user account. How to start with CoGe. Just want to play with a genome. Getting CoGe to run.

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TARGeT

TARGeT: Tree Analysis of Related Genes and Transposons. Yujun Han*, James Burnette* , and Susan Wessler*. Center for Human Genome Variation, Duke Univeristy. Department of Botany and Plant Sciences, University of California Riverside Nucleic Acids Research Article. Choose your TARGeT start page:. TARGeT using Approximately-Maximum-likelihood with FastTreeMP. TARGeT using blastn with DNA query. TARGeT using tblastn with Protein query. TARGeT using Neighbor Joining with TreeBest. Browser and the latest Java.

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