Download presentation
Presentation is loading. Please wait.
Published byTobias Dorsey Modified over 8 years ago
1
Bioinformatics What is a genome? How are databases used? What is a phylogentic tree?
2
The Genome Every organism, including man, is specified by a genome. A genome is composed of DNA segments, called genes. Genes code for proteins http://www.bio.tamu.edu/synecho/progress.html
3
Bioinformatics is used for… Determining evolutionary relationships between organisms Looking at locations of particular genes Crop/Pharmaceutical Bioengineering Medical research
4
Bioinformatics is used for…. Making new drugs Crop bioengineering Gene sequencing Making phylogenetic trees
5
The Human Genome Project Began in the year 2000, published report in 2001 (Nature) Goal: to sequence all 20,000-25,000 genes on all the chromosomes in the human body New research is focusing on bioenergy— –developing plant feedstocks (fast-growing plants bred to produce electricity or liquid fuels) –using microorganisms (like bacteria) to break down cellulose in plant cell walls –converting sugars into biofuels.
6
Databases are… a storehouse of organized, indexed computerized data
7
Databases are used to … locate a gene within a sequence predict protein structure and/or function cluster protein sequences into families of related sequences view and analyze the data on millions of genomes
8
Step 1: Go to IMG Home Page Go to Find Genes
9
Step 2: Click on BLAST
10
Step 3: Copy and paste a nucleotide or protein sequence This is your query sequence
11
Step 4: BLAST sequence Take the top hit and click on it: this will give you a list of the genomes with the most similarity to your query sequence
12
Step 5: Click on the top hit
13
Step 6: Look at Gene Detail OID number Name of protein
14
Look at “gene neighborhood” Red shows query gene
15
Step 7:Click on IMG Genome BLAST
16
Step 8: Choose a Phylum or organism to BLAST against
17
Step 9: Set Maximum E-value Run BLAST The lower this number is, the more significant the alignment is between the query sequence and the other genomes you are comparing it against A low E Value shows genes with the most homology Run BLAST
18
Look at Genome Blast Results
19
Blast hits on a particular sequence
20
Look at: Alignment and E-values O= orthologs- genes from different species which are similar P= paralogs- genes from the same species which are similar
21
For a detailed view of alignment,click on Do Alignment: Letters denote amino acids; colors denote type of amino acid Dashed lines indicate deletions Look down this column- what do you notice?
22
Categories of amino acids
23
Homologs Gene sequences that are similar and show a close evolutionary relationship Two types of homologs: –Paralogs- similar gene sequences between members of the same species –Orthologs- similar gene sequences between 2 different species
24
10. Click on the hits with the best alignment
25
11. Add Selections to Gene Cart
26
12. Click: Show Gene Neighborhoods
27
13. Gene of interest is shown in red Look at colored genes next to gene of interest Gene of interest
28
14. To make a phylogenetic tree, go to Phylogeny.fr Copy and Paste amino acid sequence Click submit
29
15. Click Blast Explorer Paste sequence Click submit
30
A phylogenetic tree of cyanobacteria with homology for a particular gene sequence
Similar presentations
© 2025 SlidePlayer.com. Inc.
All rights reserved.