1- Search for homologous sequences with BlastExplorer
Blast enables to search for sequences similar to a particular sequence. BlastExplorer is a webbased tool enabling to select homologous sequences among hits from Blast results.
Go the Blast Explorer
website http://www.phylogeny.fr/version2_cgi/one_task.cgi?task_type=blast.
And perform a BlastP against the NR bank (Non Redundant).
How many hits are there? How many hits are shown in the Blast results page?
Observe the distance tree generated from the 100 first hits and localize the query sequence.
a) Selection of homologous sequences within dicotyledons.
Extend the level of taxonomic colorization and select sequences of dicotyledons.
Update the tree taking into account your selection. What are the different taxonomic
levels which are colorized now? Eliminate potential paralogs and update the tree.
b) Selection of homologous sequences within the Oryza genus
Display again the first 100 hits. Select sequences having a score higher than 200 and
update the tree. Now, unselect branchs of other genus and update the tree. Go the the
alignment of sequence of O. longistiminata. Select sequences so that we have only one
representing sequence par Rice species and update the tree and retrieve sequences.
c) Selection of homologous sequences within Viridiplantae
We are going to select more distant sequences. Click on the « Large selection box »
and test the effect of the « e-value » filter on the number of active sequences. Fix the
filter to 1.e-10 and select 10 plant sequences among the taxonomy in order to cover a
large evolution panel.
At this point, we assume to hold a set of homologous sequences that will be used for a
phylogenetic analysis.
2- Phylogenetic analysis with Phylogeny.fr
Send your plant homologous sequences to the « One-click » pipeline of Phylogeny.fr.
a) Multiple alignment
Observe the different alignment formats: Phylip, FASTA, and Clustal.
Observe the multiple alignment with the Jalview software.
b) Alignment cleaning
GBlocks eliminates poorly aligned positions and divergent regions of an alignment of
DNA or protein sequences. These positions may not be homologous or may have been
saturated by multiple substitutions and it is convenient to eliminate them prior to
phylogenetic analysis.
What is the proportion of conserved positions in the alignement after cleaning by
GBlocks.
c) Phylogenetic tree
Observe the Newick format, tree file provided by PHYML.
Observe the phylogenetic tree with ATV.
d) Tree rendering
TreeDyn enables to draw a phylogenetic tree as an image from a Newick file.
Test the cladogram radial and circular representations.
Test branch renaming and colorization.