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| Collective Resources and Tutorials
This is a collection of links to all of the tutorial and resource pages created by the students from the fall 2009 class of BE131 as part of their final projects.
Table of Contents:
JBrowse Setup and Basic Annotations
- Final Project J Browse Gen Bank Parsing created by Sushant Sundaresh
- wubi-ubuntu quick install created by Sushant Sundaresh
- How to format JBrowse-readable GFF (including url-linking issues) by Shicong Xie on 08 Dec 2009
- Windows JBrowse Setup by Kamran Ali
- GC Content WIG from FASTA by Ashray Urs
- Adding GLIMMER gene prediction to your Jbrowse by Ashray Urs
- Using the Config File to Load Features by Kamran Ali
- Adding tacg-generated RE site track by Shicong Xie
- How to add the "possible primers" track to JBrowse? by Peerapong Pornwongthong
- Semi-Automated Primer -> GFF for specific regions of interests by Shicong Xie
- How to convert GenBank to GFF3 format used for Jbrowse? by Peerapong Pornwongthong
OMGBrowse Implementation of JBrowse
- OMGBrowse - A free implementation of JBrowse where anybody can create an account and start annotating created by Arthur Yu, Jordi Silvestre-Ryan, David Tam, and Matt Dewitt
- Basic genome, and gene annotations in OMGBrowse emailed by Arthur Yu to class google group on 12/6/09
Sequence Alignment Tutorials
- Constructing and Viewing Protein Alignments by Daniel Yang
- Final Project J Browse Quantitative Alignment Tutorial created by Sushant Sundaresh
- Multiple Alignment via CLUSTAL and conversion to WIG file by Ashray Urs
To contact all students from the class who have opted in, please email: bioe131_fall2009@googlegroups.com
To see the collective genome wikipage that links to all of the class projects go to the Fall09 Virus Phylogenetic Tree
-- MadhviVenkatesh - 07 Dec 2009 |
