Notes

yrGate best evidence is complete CDNA - next best is various transcripts - then homologous proteins - finally computer predictions transcripts in red - use these for evidence to build a structure yellow are conserved proteins select structures from parts above to build structure Check the number of nucelotides and amino acids Blastp to see if you get matches build GAEVAL score

Assignment

For this class session, we looked at online databases that are sources of not only sequence information, but also annotations relaying important information that goes beyond just the nucleotide construction. Examples of these databases are:

plantgdb

flybase

plasmodb

One of the most interesting features that is offered on some of these databases is the “Community Annotation” feature which allows individuals to view annotations and edit them. The annotations on the pages are generated via the application of algorithms and programs to generally predict features such as coding regions, introns/ exons, and open reading frames. However, the methods used for the global identification of these features are not perfect, and errors in annotation are common. With the recruitment of the scientific community and interested members of the general public, these annotations can be refined and thus improve the accuracy of the database.

These pages list the annotations available for review in a basic graphical user interface

And some offer a wide assortment of tools, tutorials, and guides to help you with your work.

The tools are extensive, and there are many factors to consider when making an edit.

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b2gof15/students/bradbows/class_sessions/2015.10.15.txt · Last modified: 2015/10/20 13:44 by bradbows
 
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