Bioinformatics Flashcards
What is genome annotation?
A process of identifying functional elements along the sequence of a genome. It is important because the sequencing of DNA procedures sequences of unknown function
- Go to: http://www.ncbi.nlm.nih.gov
- Use the dialogue box to select genome
- Type in the name of the organism whose genome you desire (e.g. Phi X174)
- Click on go to do the search
- At the end of the search, a few accession numbers with the names of the organisms are displayed
- Select Enterobacteria phage phX174, complete genome accession no. NC_001422. The diagram below will be displayed.
- This is a circular ssDNA with 5386nt & 11 genes . Explore by clicking and sliding
How to perform BLASTN search of the NR database at the NCBI site?
- Conn3ct to the NCBI BLAST homepage with your browser. Http://www.NCBI.nlm. Nih.gov/BLAST/
- In the nucleotide section on the page choose the link to the Nucleoride-nucleotide BLAST (blastn) search algorithm
- Enter your DNA sequence into the SEARCH text box
- Select the default (nr) database in the choose database menu box
- Click on the BLAST! Button to perform the search
How to translate DNA/RNA into protein Using BLASTX?
- Connect to the NCBI Homepage with your browser. http://www.ncbi.nlm.gov/BLAST/
- On the page under Basic BLAST, choose the link to blastx search algorithm
- Enter your nucleotide sequence in the Search text box
- Select the default (nr) database in the Choose database menu box
- Click on the BLAST button to perform the search
How to perform a BLASTP search of the NR database at the NCBI site?
- Connect to the NCBI BLAST homepage with your browser. Http://www.ncbi. nlm.nih.gov/BLAST/
- In the protein section on the page, choose the link to the Protein BLAST (blastp) search algorithm
- Enter your protein sequence into the Search text box
- Select the default (nr) database in the choose database menu box
- Click on the BLAST! button to perform the search
How to search for the homologues of a gene?
Suppose we want to find the homologue of the human insulin gene
- Connect to www.ncbi.nlm. nih.gov
- Select homology from the list of resources to the left of the page and
- From the homology page, use the drop down menu to select homologene data base
- Type in the name of the gene whose homologue you desire
- Start search
How to use multiple sequence alignment & phylogenic relationships
To do this, we need a tool such as COBALT or CLUSTA W
- connect to http://www. NCBI.nih.gov/tools/cobalt/cobalt.cgi?link_loc=BlastHomeAd
- Copy & paste the accession #s of the sequences you wish to align
- Click on the align button to start aligning
- After alignment, draw a phylogenies tree
How can genes be searched for by ORF identification?
- Go to Expert Protein Analysis System(ExPASY) website at: https://web.expasy.org/translate/
- Copy and paste your sequence into the box and translate it
- Do a visual inspection and select ORFs based on the criteria already discussed
4 click on any potential start codon of ORF to generate a predicted primary structure of the protein.
- At the middle of the page, click on BLAST to compare your sequence against known sequences in the protein data base
- Go to the National center for biotechnology information (NCBI) website at http://www.NCBI.nlm. NIH .gov
7 select data and software
- Under tools you will find ORF finder and click on it. You may go directly to ORF finder at NCBI at: http://www.ncbi.nih.nlm.gov/gorf/gorf.html
- https://www.ncbi.nlm. Gov/orffinder/
Copy and paste sequence in the search box
Click on ORF find and wait for a few seconds
A second map of your region will be displayed with potential ORFs
Click on these to display the predicted primary sequence for that ORF to be shown on a new screen
At the top of the screen click the BLAST box and the protein sequence will be tested for matches against known sequences
