Page last modified 16:30, 12 Mar 2010 by goodnerbw
Table of contents
No headersBrad 3/11/2010: I have attached a Word document that has the BLOSUM62 and PAM250 substitution matrices shown and a link to some course pages from another university that describes how the matrices were constructed.
Brad 3/12/2010: I have attached several other resources below:
My slides
The lab manual I gave my students on the annotation project this year (Streptobacillus; 2 genes/student)
The lab manual I gave my students on the annotation project last year (Planctomyces; pathway/team of students)
Example of a phylogenetic profiler result
My own example of pathway-driven gene annotation (TCA cycle in Planctomyces limnophilus)
Tree-thinking Resources
Papers:
- Tag page
- What links here
Files 15
| File | Size | Date | Attached by | |||
|---|---|---|---|---|---|---|
 | Substitution Matrices.doc No description | 27.5 kB | 21:43, 11 Mar 2010 | goodnerbw | Actions | |
| Baum_05.pdf The Tree-Thinking Challenge | 5.82 MB | 11:13, 12 Mar 2010 | sdonovan | Actions | |
| Goodner2010Handouts.ppt No description | 5.26 MB | 12:43, 12 Mar 2010 | goodnerbw | Actions | |
| StreptobacillusAnnotationProject.doc No description | 81.5 kB | 12:43, 12 Mar 2010 | goodnerbw | Actions | |
| Nature Methods HMM.pdf Hidden Markov models | 103.56 kB | 14:04, 12 Mar 2010 | kscott@cas.usf.edu | Actions | |
| The Scientist _ HMM.pdf More on HMMs | 154.3 kB | 14:04, 12 Mar 2010 | kscott@cas.usf.edu | Actions | |
| MUSCLE.pdf Describes MUSCLE alignment process | 399.58 kB | 14:04, 12 Mar 2010 | kscott@cas.usf.edu | Actions | |
| 01_Protein structure and evolution.pdf Wshp presentation on protein evolution | 734.6 kB | 14:05, 12 Mar 2010 | kscott@cas.usf.edu | Actions | |
| 02_Tools for inferring protein structure and function.pdf Wshp presenation on motif, etc. tools | 522.9 kB | 14:05, 12 Mar 2010 | kscott@cas.usf.edu | Actions | |
| 03_alignments_MUSCLE.pdf Wshp presentation on sequence alignments | 1050.69 kB | 14:05, 12 Mar 2010 | kscott@cas.usf.edu | Actions | |
| PlanctomycesAnnotationProject.doc No description | 75.5 kB | 15:59, 12 Mar 2010 | goodnerbw | Actions | |
| PhylogeneticProfilerExample UTI Ecoli.xls No description | 33.5 kB | 15:59, 12 Mar 2010 | goodnerbw | Actions | |
| Example of Pathway Driven Gene Annotation.doc No description | 50 kB | 16:30, 12 Mar 2010 | goodnerbw | Actions | |
| Hemoglobin betas.fas FASTA file of unaligned hemoglobin beta subunits | 3.08 kB | 12:13, 13 Mar 2010 | kscott@cas.usf.edu | Actions | |
| Tree from hemoglobin data.pptx Tree from FASTA file, after aligning | 157.44 kB | 12:13, 13 Mar 2010 | kscott@cas.usf.edu | Actions | |
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