The guide:


Step 1: obtaining a sequence of interest

If you have a sequence of interest proceed to step 2.

Once you obtained your sequence of interest (YSI) save it in a file using the "Save As" command of your browser.


Step 2. Identify ORFs and translate into protein


Step 3. Find similar sequences in the databases


Step 4. Do a global alignment of your sequence vs similar sequences

Even though, the previous Blast search engines provide local alignments (alignments of the similar regions), a global alignment (alignment of all regions) may help getting a better insight about your target sequence. For example, "gain" or "loss" of functional domains (ivis-a-vis) a reference sequence.


Step 5. Look for gene families


Step 6. Look for the presence of specific patterns in your protein


Step 7. Determine the putative structure of your protein


Step 8. Obtain information about function of related proteins

To understand the function of your target protein, it may be useful to gather information about proteins that share similar structural or sequence elements. Thus, a PubMed search using as keywords the names of the proteins revealed by the various steps of this analysis, may provide you with functional insight about your protein.


Step 9. Input your sequence into an "alert" server