生物信息学课件5PhylogeneticTree.pptVIP

All because of Darwin… Trees, Oh, lovely trees… The mathematical definition of a tree A graph is a set of points with lines connecting some of the points. The points are called nodes or vertices, and the lines are called edges. The number of edges at a node is the degree of that node. Path in a graph is sequence of nodes connected by edges. A graph is connected if every two nodes have a path between them. A simple cycle is one that does not repeat any nodes except for the first and the last. A graph is a tree if it is connected and has no simple cycles. The nodes of degree 1 in a tree are called the leaves. A specially designated node is called the root. How to make a tree given leaves? Jukes and Cantor Model Homework Make a webpage, use a Textarea to accept two sequences in the fasta format, submit, use a server-side php program to parse the sequences into k-length words, store the words from one sequence in a table named “query” in your MySQL database, and the words from the other in a table named “dbseq”, also display the results on another page of the browser. Deadline: April 20, 2011 Hints * * * * * * * * * * * * * * * * * * * * * * * * * * * * * hemolectin 3843 aa Product of CG15284 served as a partner of burs protein to form bursicon heterodimer CG15284 burs burs/ CG15284 PB ganglia extract Bursicon, the insect cuticle hardening hormone, is a heterodimeric cystine knot protein that activates G protein-coupled receptor LGR2 Position-Specific Iterated PHI- PSI-BLAST Find and store your own PSSM for the future search Position Specific Score Matrix (the ASCII-encoded format) Save ? future pattern search Where to find it? Example of searching for short, nearly exact matches What should I do in “APRIL” Ala-Pro-Arg-Ile-Leu 100 hits No significant similarity found Query: 1 APRIL 5 APRIL Sbjct: 21 APRIL 25 Protein Domain Search using NCBI and other web sources Reverse Position Specific BLAST: Reverse of PSI (Position-Specific Iterated)-BLAST