User: Cupton

gravatar for Cupton
Cupton40
Reputation:
40
Status:
New User
Location:
Victoria, BC, Canada
Website:
http://Virology.uvic.ca/
Twitter:
cupton1
Last seen:
2 months, 2 weeks ago
Joined:
8 years, 9 months ago
Email:
c*****@uvic.ca

Develop software for bioinformatics analysis of viral genomes (large DNA viruses)

Posts by Cupton

<prev • 7 results • page 1 of 1 • next >
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Answer: A: Looking for degenerate primer sequences in a multi-fasta file
... our tools: Sequence searcher https://4virology.net/virology-ca-tools/sequence-searcher/ Base-By-Base https://4virology.net/virology-ca-tools/base-by-base/ could work, depends how many fasta seqs you have ...
written 12 weeks ago by Cupton40
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Comment: C: Standalone Multiple Sequence alignment tool
... Agreed. We use MAFFT within our MSA editor (Base-By-Base) ...
written 15 months ago by Cupton40
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Comment: C: Standalone Multiple Sequence alignment tool
... Base-By-Base uses ClustalO, Muscle or MAFFT for alignments ...
written 15 months ago by Cupton40
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Answer: A: Standalone Multiple Sequence alignment tool
... Jalview is great, but focuses on proteins. Have a look at Base-By-Base: https://virology.uvic.ca/virology-ca-tools/base-by-base/ This can handle genes, proteins, viral genomes (up to 400 kb). It has a different set of modules than Jalview. It makes editing MSAs easy and displays the differences ...
written 15 months ago by Cupton40
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Zoomable phylogenetic tree as interface to mySQL database
... I have 350 virus genomes in a mySQL database. I want to use a zoomable phylogenetic tree as the interface to the database instead of the long list in our java database GUI. ie the tree has to let me select the genomes. I can produce the Newick data from aligning DNA polymerases. There's about 15 gen ...
mysql written 15 months ago by Cupton40 • updated 15 months ago by Joseph Hughes2.7k
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Answer: A: Plylogenetic tree construction
... Be sure to view and your alignment so you can see errors. ...
written 15 months ago by Cupton40
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What Tool Should I Use To Assemble Data Produced By A 454 Sequencer?
... What do you like for assembling paired-end #454 sequence data? (for 200kb assemblies) ...
assembly open next-gen sequencing written 8.8 years ago by Cupton40 • updated 8.1 years ago by Ketil3.9k

Latest awards to Cupton

Autobiographer 15 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 8.8 years ago, created a question with more than 1,000 views. For What Tool Should I Use To Assemble Data Produced By A 454 Sequencer?
Student 8.8 years ago, asked a question with at least 3 up-votes. For What Tool Should I Use To Assemble Data Produced By A 454 Sequencer?

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