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CUB-DB Blog | Updates and news for the Codon Usage Bias DatabaseWelcome to the CUB-DB blog.
http://cubdb.wordpress.com/
Welcome to the CUB-DB blog.
http://cubdb.wordpress.com/
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CUB-DB Blog | Updates and news for the Codon Usage Bias Database | cubdb.wordpress.com Reviews
https://cubdb.wordpress.com
Welcome to the CUB-DB blog.
cubdb.wordpress.com
All caught up! | CUB-DB Blog
https://cubdb.wordpress.com/2016/08/15/all-caught-up
Updates and news for the Codon Usage Bias Database. August 15, 2016. August 15, 2016. Amazingly, the Codon Usage Bias Database is all caught-up. This hasn’t been the case in years. It is now up-to-date with NCBI’s Microbial Complete Genomes Database. To understand why this is so unusual, let’s examine the source of genome data for my database. The download process begins with NCBI’s list of Microbial Genomes ( Bacterial and Archael. So why is it so difficult to keep up-to-date? The New Blog Page. This is...
Blog | CUB-DB Blog | Updates and news for the Codon Usage Bias Database
https://cubdb.wordpress.com/blog
Updates and news for the Codon Usage Bias Database. I knew it couldn’t last. August 18, 2016. Just checked. There are now 45 new microbial genomes and 236 existing genomes that have been updated. Ah well…. August 15, 2016. August 15, 2016. Amazingly, the Codon Usage Bias Database is all caught-up. This hasn’t been the case in years. It is now up-to-date with NCBI’s Microbial Complete Genomes Database. I identify all complete genomes, and pull their annotated files to my server. The New Blog Page. This is...
The New Blog Page | CUB-DB Blog
https://cubdb.wordpress.com/2016/08/09/new-blog-page
Updates and news for the Codon Usage Bias Database. The New Blog Page. August 9, 2016. August 12, 2016. Welcome to the new CUB-DB Blog page. If you track the old page, you have probably noticed that it is no longer active. stay tuned for news from your friendly neighborhood codon usage guy. Next step–update the link on the actual CUB-DB website. Leave a Reply Cancel reply. Enter your comment here. Fill in your details below or click an icon to log in:. Address never made public). Footer Three Menu Widget.
I knew it couldn’t last | CUB-DB Blog
https://cubdb.wordpress.com/2016/08/18/i-knew-it-couldnt-last
Updates and news for the Codon Usage Bias Database. I knew it couldn’t last. August 18, 2016. Just checked. There are now 45 new microbial genomes and 236 existing genomes that have been updated. Ah well…. Leave a Reply Cancel reply. Enter your comment here. Fill in your details below or click an icon to log in:. Address never made public). You are commenting using your WordPress.com account. ( Log Out. You are commenting using your Twitter account. ( Log Out. Notify me of new comments via email.
About | CUB-DB Blog
https://cubdb.wordpress.com/about
Updates and news for the Codon Usage Bias Database. Follow to find-out what’s new with the CUB-DB. This is a text widget. The Text Widget allows you to add text or HTML to your sidebar. You can use a text widget to display text, links, images, HTML, or a combination of these. Edit them in the Widget section of the Customizer. Visually explore codon bias levels across entire microbial genomes. Footer Three Menu Widget. Create a free website or blog at WordPress.com.
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Codon Usage Bias Database (CUB-DB)
http://csweb1.cs.umt.edu/future.shtml
Future plans for the CUB-DB. What's in and out of the DB. The big thing slowing down the process is making sure we have a good backup process for the database. It doesn't seem very efficient to shut-down the DB every night and spend an hour or more dumping all of the data into a monolithic backup. When the DB is only 50Meg, then a mysqldump works just find. But 40Gig? I want to add strand criterion to my measures. This will require knowledge of where the chromosomal replication origin site. It currently ...
Codon Usage Bias Database (CUB-DB)
http://csweb1.cs.umt.edu/index.shtml
Codon Usage Bias Database (CUB-DB) and Explorer. The Codon Usage Bias Database is a showcase for my bias measures, modified Self-Consistent Codon Index (mSCCI) and a direct search approach for codon adaptiveness (weights) using a genetic algorithm (GA). The first modifies the Carbone et al. Algorithm to direct it toward translational efficiency bias instead of the dominant bias ( mSCCI, Raiford et al. The database currently has a size of approximately 130Gig and is comprised mostly of text files residing...
Codon Usage Bias Database (CUB-DB)
http://csweb1.cs.umt.edu/tutorial.shtml
Codon Usage Bias Tutorial. Methods for Isolating Translational Efficiency Bias. Frequency of usage of optimal codons (FOP). This frequency was found to be highly correlated with protein abundance. All the rules except tRNA availability were the same from species to species and the translational efficiency attained through tRNA abundance was presumed to be the driving force behind the correlation. Codon Adaptation Index (CAI). Methods for Simply Measuring the Degree of Bias. Effective Number of Codons (Nc).
Codon Usage Bias Database (CUB-DB)
http://cub-db.cs.umt.edu/tutorial.shtml
Codon Usage Bias Tutorial. Methods for Isolating Translational Efficiency Bias. Frequency of usage of optimal codons (FOP). This frequency was found to be highly correlated with protein abundance. All the rules except tRNA availability were the same from species to species and the translational efficiency attained through tRNA abundance was presumed to be the driving force behind the correlation. Codon Adaptation Index (CAI). Methods for Simply Measuring the Degree of Bias. Effective Number of Codons (Nc).
Codon Usage Bias Database (CUB-DB)
http://cub-db.cs.umt.edu/index.shtml
Codon Usage Bias Database (CUB-DB) and Explorer. The Codon Usage Bias Database is a showcase for my bias measures, modified Self-Consistent Codon Index (mSCCI) and a direct search approach for codon adaptiveness (weights) using a genetic algorithm (GA). The first modifies the Carbone et al. Algorithm to direct it toward translational efficiency bias instead of the dominant bias ( mSCCI, Raiford et al. The database currently has a size of approximately 130Gig and is comprised mostly of text files residing...
Codon Usage Bias Database (CUB-DB)
http://cub-db.cs.umt.edu/future.shtml
Future plans for the CUB-DB. What's in and out of the DB. The big thing slowing down the process is making sure we have a good backup process for the database. It doesn't seem very efficient to shut-down the DB every night and spend an hour or more dumping all of the data into a monolithic backup. When the DB is only 50Meg, then a mysqldump works just find. But 40Gig? I want to add strand criterion to my measures. This will require knowledge of where the chromosomal replication origin site. It currently ...
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Father and son discover cub scouting. A Few Things to Share. December 22, 2009. Photo courtesy of theirhistory. We’ve been a scouting family now since mid-September 2009. As a new cub dad and volunteer, I’ll share a bit of what we have learned thus far. 1 Reinforcing the uniform. 2 What to do with the Trails End Popcorn tin. Once you get into cub scouting, you’ll want to keep the uniform together. 3 There’s an app for that! 4 Cub Scout podcasts. A Season of Scouting Begins. December 1, 2009. Earlier in t...
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CUB-DB Blog | Updates and news for the Codon Usage Bias Database
Updates and news for the Codon Usage Bias Database. Welcome to the CUB-DB blog. You probably got her from the main CUB-DB website. Follow to find-out what’s new with the CUB-DB. I knew it couldn’t last. Just checked. There are now 45 new microbial genomes and 236 existing genomes that have been updated. Ah well…. Read more I knew it couldn’t last. Read more All caught up! The New Blog Page. Read more The New Blog Page. Download csv files with lists of genes and their codon usage bias levels.
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