User: Cupton

gravatar for Cupton
Cupton70
Reputation:
70
Status:
Trusted
Location:
Victoria, BC, Canada
Website:
http://Virology.uvic.ca/
Twitter:
cupton1
Last seen:
4 weeks, 1 day ago
Joined:
9 years, 6 months ago
Email:
c*****@uvic.ca

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

Posts by Cupton

<prev • 12 results • page 1 of 2 • next >
1
vote
1
answer
112
views
1
answers
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 29 days ago by Cupton70
1
vote
1
answer
165
views
1
answers
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 29 days ago by Cupton70
1
vote
0
answers
206
views
0
answers
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 5 weeks ago by Cupton70
0
votes
1
answer
161
views
1
answers
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 10 weeks ago by Cupton70
0
votes
0
answers
209
views
0
answers
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 weeks ago by Cupton70
0
votes
1
answer
327
views
1
answers
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 months ago by Cupton70
0
votes
6
answers
1.7k
views
6
answers
Comment: C: Standalone Multiple Sequence alignment tool
... Agreed. We use MAFFT within our MSA editor (Base-By-Base) ...
written 2.0 years ago by Cupton70
0
votes
6
answers
1.7k
views
6
answers
Comment: C: Standalone Multiple Sequence alignment tool
... Base-By-Base uses ClustalO, Muscle or MAFFT for alignments ...
written 2.0 years ago by Cupton70
0
votes
6
answers
1.7k
views
6
answers
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 2.0 years ago by Cupton70
2
votes
1
answer
565
views
1
answer
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 2.0 years ago by Cupton70 • updated 2.0 years ago by Joseph Hughes2.8k

Latest awards to Cupton

Autobiographer 2.0 years ago, has more than 80 characters in the information field of the user's profile.
Popular Question 9.6 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 9.6 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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1375 users visited in the last hour