User: Cupton

gravatar for Cupton
Cupton70
Reputation:
70
Status:
Trusted
Location:
Victoria, BC, Canada
Website:
http://Virology.uvic.ca/
Twitter:
cupton1
Last seen:
8 months, 2 weeks ago
Joined:
10 years, 3 months ago
Email:
c*****@uvic.ca

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

Posts by Cupton

<prev • 13 results • page 1 of 2 • next >
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Comment: A: Matching sequences from PDB with sequence from Alignment.
... Doesn't Jalview do this through its GUI? perhaps you don't want a manual procedure... ...
written 8 months ago by Cupton70
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Answer: A: Purines and pyrimidines in frame shift mutations
... Sequencing errors are common in homopolymers. If I see a FS in a homopolymer, my first check is the raw sequencing data. ...
written 9 months ago by Cupton70
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Comment: C: Interpret genome alignment results
... Exactly!! Only translate and compare protein-coding regions. For non-coding regions, DNA similarity can be high but when ERRONEOUSLY translated, the "protein" sequences could be from different frames and therefore very low similarity. Again, only translate and compare protein-coding regions. ...
written 9 months ago by Cupton70
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Comment: C: Multiple Sequence Alignment viewers or How to Build a Conservation Plot
... Base-By-Base is on the wikipedia list. (our tool), has several way to summarize the similarity ...
written 10 months ago by Cupton70
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Answer: A: How to use mafft to do large scale sequence alignment?
... Throw out identical sequences first.... We made this tool years ago: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694821/ Not sure where the code is these days. ...
written 11 months ago by Cupton70
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Comment: C: Large viral Genome Alignment Software
... Use MAFFT; then view the results in Base-By-Base. This can highlight diffs to a reference. Disclaimer: BBB is our tool. ...
written 11 months ago by Cupton70
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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 21 months ago by Cupton70
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Comment: C: Standalone Multiple Sequence alignment tool
... Agreed. We use MAFFT within our MSA editor (Base-By-Base) ...
written 2.8 years ago by Cupton70
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Comment: C: Standalone Multiple Sequence alignment tool
... Base-By-Base uses ClustalO, Muscle or MAFFT for alignments ...
written 2.8 years ago by Cupton70
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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 2.8 years ago by Cupton70

Latest awards to Cupton

Autobiographer 2.8 years ago, has more than 80 characters in the information field of the user's profile.
Popular Question 10.3 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 10.3 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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