Genetic databases for analyzing genomic information.

[Phernando]

1. To seach for information about a gene: function, location and structure, RNA or protein; visualize protein coding sequence and untranslated regions, obtain cDNA sequence; links to other databases.

 

NCBI

https://www.ncbi.nlm.nih.gov/

 

Select database from the dropdown menu and search for the gene or protein of interest using the official name or the reference number.

 

2. To identify the gene/protein based on the sequence; search for homology between two species

 

Blast

https://blast.ncbi.nlm.nih.gov/Blast.cgi

 

Copy the sequence of interest and paste it into the blast window. Select pblast for protein or nblast for nucleotide sequences; then click BLAST. For comparison between species, paste sequence of mouse actin gene, for example and paste it next to human genome. Result will show % homology, the e value, and the alignment.

 

3. To find information about a gene in cartoon or sequence form: splice variants, sequence variants. To visualize the protein coding and non-coding variants and to obtiain links to single nucleotive variants/polymorphisms.

 

Ensembl

http://useast.ensembl.org/index.html

 

Search for the gene, visualize the splice variants in a table or graphic format. Select sequence (on the left task panel) - configure page--> show variants/polymoerphisms with links.

 

4. To display information about protein structure in an interactive manner, to visualize functional domains

 

RCSB ProteinDataBank PDB

http://www.rcsb.org/pdb/home/home.do

 

Search for the protein, select 3D view, rotate, zoom in and out. switch tabs or scroll down to find information on functional domains and the secondary structure of each domain.

 

5. To find information on copy number variants or expression variants in different types of cancers.

 

UCSC Cancer Genome Browser

https://genome-cancer.ucsc.edu/

 

Load database with patient datasets on a specific type of cancer. Visualize statistical analysis of copy number or expression variants according to location on each chromosome or choose variations in specific genes in the patient sample.

 

6.To find information about a disease, genetic contribution, Mendelian inheritance if observed, clinical features, research and treatment

 

OMIM

http://omim.org/

 

Enter gene name and display relevant properties, including pathology or diseases associated with mutations in the genes.

 

7.To align multiple sequences in order to assess/compare/quantify or evaluate sequence conservation. To construct a

phyogenetic tree.

 

Clustal Omega

http://www.ebi.ac.uk/Tools/msa/clustalo/

 

copy sequences with >in_front_of_the_gene_ID no spaces (or protein), select protein of nucleotide in the dropdown menu. visualize the extent of conservation; can generate phylogenic trees to see the common encestors and divergence

 

8. To visualize the evolutionary distance between species

 

Phylogeny Fr

http://www.phylogeny.fr/

 

Use multiple sequence alignment from the Clustal Omega to create a Newick file and then visualize the real evolutionary relationship and distance

 

9. To compare the phylogenic relationship of species of oral microbiota based on sequence of 16S rRNA geneTo

 

Human Oral Microbiome Database

http://www.homd.org/

 

Select species, blast.

To find information about a gene in cartoon or sequence form: splice variants, sequence variants. To visualize the protein coding and non-coding variants and to obtiain links to single nucleotive variants/polymorphisms. Ensembl http://useast.ensembl.org/index.html Search for the gene, visualize the splice variants in a table or graphic format. Select sequence (on the left task panel) - configure page--> show variants/polymoerphisms with