Bioinformatics & Genomics Lecture 3 PDF

Bioinformatics & Genomics Lecture 3 By: Fatma Alshohomi This lecture will cover ❖ Web-based resources (NCBI, OMIM) Gene database: NCBI Role of NCBI 1) Maintenance of biological databases whether primary or secondary. It includes GENEBANK. 2) NCBI provides the...

Bioinformatics & Genomics Lecture 3 By: Fatma Alshohomi This lecture will cover ❖ Web-based resources (NCBI, OMIM) Gene database: NCBI Role of NCBI 1) Maintenance of biological databases whether primary or secondary. It includes GENEBANK. 2) NCBI provides the data retrieval systems such as ENTREZ. 3) Provides computational sources for the analysis of the GENEBANK data and other biological data. NCBI Home page NCBI: Difference between tools and Databases NCBI tools 1. BLAST Basic local alignment search tool program Finds regions of local similarity between protein or nucleotide sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. How to start use NCBI? Looking for more information about specific gene For example: INS gene 2. Write the name of the 1. Chose gene or its symbol 3. Click Search Gene Looking for more information about specific gene Information about gene when you click on it The type of species is human Looking for the gene in different species  Scroll down the page An alternative symbol or name for part of the Its location and sequence of a known gene Genomic NC Showing in which species, this gene is present Each gene has a specific ID in In next different slides, we’ll species know it  Next page When you clink on this choice, you will get Summary about the gene Next page If you scroll down the page, Moving to another software or website OMIM Database Online Mendelian Inheritance in Man (OMIM) A catalog of human genes and genetic disorders. Curated database containing descriptions of relationship between phenotypes, their genes, and variations including: 1. Small Nucleotide Polymorphisms (SNPs). 2. Copy number variations (CNVs). OMIM Homepage DISORDERS DEALT WITH IN OMIM One of the best websites for detailed and updated information of genetic diseases. Contains disorders which are inherited in a Mendelian fashion. It does not include conditions resulting from chromosomal aberrations. OMIM NUMBERS Each genetic disorder has been allotted a unique six digit OMIM number. The first digit indicates the mode of inheritance of the disorder. 1. (100000- ) Autosomal dominant loci or phenotypes 2. (200000- ) Autosomal recessive loci or phenotypes 3. (300000- ) X-linked loci or phenotypes 4. (400000- ) Y-linked loci or phenotypes 5. (500000- ) Mitochondrial loci or phenotypes 6. (600000- ) Autosomal loci or phenotypes HOW IS A DISEASE ACCESSED ON OMIM? The basic search involves typing in the name of a disease, a chromosome number or a gene symbol, and clicking on ‘Go’. In fact, almost 1900 entries show up for the word ‘skin’, giving one some idea of how many genetic disorders involve the skin. For example, a search for ‘dermatitis’ shows about 226 entries which include various subtypes of dermatitis and related genetic conditions. For example If you write Hemophilia in search tab of the OMIM homepage, then you will get this page OMIM GENE MAP & OMIM MORBID MAP The OMIM gene map lists disorders gene wise, starting with chromosome 1p and ending with 22q, along with the X and Y chromosomes. Diseases which have been linked to specific genes on these chromosomes are available in this map. This map can be searched using the chromosome number, gene symbol or name of disorder. The OMIM morbid map is an alphabetical list of disorders and their cytogenetic locations. It can be searched in the same fashion as the OMIM gene map. OTHER FEATURES of OMIM A click on OMIM statistics lets one know the total number of entries available on that day. The website also provides details of changes, additions and deletions on a monthly basis since its inception in 1995. OMIM also provides links to Pubmed, the Human Genome websites and other related genetic research websites. WHAT DOES OMIM NOT PROVIDE? OMIM does not have a complete list of all genetic disorders contained in it; these have to be searched by name or symbol. It also does not provide facilities for the clinical evaluation and genetic testing of patients of suspected genetic diseases.