Lab Exercises
| lab2homologyphylogeny2-6-13.doc |
Lab 2: Homology & Phylogeny
- Find homologs and build a page on your site with all of your homologs either under your DNA or Protein page. I would list your organism, correct gene name, accession number & % identity (hyperlink the Accession number out). You can list this next to an image of the actual organism to create interest.
- Find all of your homologs and paste the FASTA formats (DNA or Protein) into one document
- Perform a ClustalOmega or ClustalW2 alignment (and try other programs)
- Build Trees using Neighbor Joining % Identity or BLOSUM62 and Average Distance % Identity or BLOSUM62 algorithms. (if you don't know what these are look up in your readings for this week and on the websites you use)
- Upload the Trees to your Website and discuss your results.
Homology:
- Homologene: http://www.ncbi.nlm.nih.gov/homologene
Multiple Alignment Programs: is generally the alignment of three or more biological sequences (protein or nucleic acid) of similar length. From the output, homology can be inferred and the evolutionary relationships between the sequences studied. I have used Clustal Omega (only for protein seqs), ClustalW2, Muscle & T-COFFEE/3D-COFFEE before.
Phylogeny Programs:
- ClustalWOmega: http://www.ebi.ac.uk/Tools/msa/clustalo/
- Phylogeny.fr: http://www.phylogeny.fr/
- TreeFam: http://www.treefam.org/
Phylogenetic Tree
Node: represents a taxonomic unit. This can be either an existing species or an ancestor.
Branch: defines the relationship between the taxa in terms of descent and ancestry.
Topology: the branching patterns of the tree.
Branch length: represents the number of changes that have occurred in the branch.
Root: the common ancestor of all taxa.
Distance scale: scale that represents the number of differences between organisms or sequences.
Clade: a group of two or more taxa or DNA sequences that includes both their common ancestor and all of their descendents.
Branch: defines the relationship between the taxa in terms of descent and ancestry.
Topology: the branching patterns of the tree.
Branch length: represents the number of changes that have occurred in the branch.
Root: the common ancestor of all taxa.
Distance scale: scale that represents the number of differences between organisms or sequences.
Clade: a group of two or more taxa or DNA sequences that includes both their common ancestor and all of their descendents.
Pasting HTML code into Weebly
How to paste stuff from a Word
file into your web pages.
Type as you normally would in Word. Now whatever you want to post on your site you need to copy and paste into a new word file. After you have done that. Save as a Webpage (this is under the File tab). Now your file will have a .htm at the end.
After you publish it you might see that the font size it too big. If this happen you have got back to Word and format in a different Font size and re-save it again like you did above.
Type as you normally would in Word. Now whatever you want to post on your site you need to copy and paste into a new word file. After you have done that. Save as a Webpage (this is under the File tab). Now your file will have a .htm at the end.
- Then go up to View>HTML Source
- The file will now look like code.
- Go to Weebly and insert a Custom HTML block on to your page.
- Copy and paste this code into the box after clicking Edit Custom HTML.
- Publish.
After you publish it you might see that the font size it too big. If this happen you have got back to Word and format in a different Font size and re-save it again like you did above.
