Electronic Notebook for Protein Sequence Analysis

The electronic notebook is a tutorial and analysis web-form consisting of a set of links to DNA and protein analysis tools combined with areas into which results and personal notes can be recorded. All the analysis tools open into a second "tools" window from which the results can be transferred into the notebook. These results and notes can be saved to a local file using the "Save the Notebook" buttons found throughout the notebook. The "Cheat now!" links open a third window in which a complete set of results have already been recorded. The electronic notebook can also be used to analyze a new DNA sequence by substituting the new sequence for the original sequence found in the DNA sequence text area.

Start here with your DNA sequence

Initial DNA Sequence

To identify any exons in the DNA sequence and generate a predicted protein sequence, click here:

GenScan


Paste your DNA sequence into the GenScan input window and press the "Run Genscan" button.
Select the protein translation with the highest exon P-values and paste this FASTA formatted output into your notebook.
 

Protein Sequence from Genscan


Genscan Results

  



To scan the protein sequence for the occurrence of motifs/patterns found in the PROSITE database, use:

ScanProsite

Paste the raw (leave off the fasta defline) protein sequence from GenScan into the ScanProsite input box, choose to
Exclude patterns with a high probability of occurrence, and press the "Start the Scan" button.
Paste the ScanProsite hit into your notebook.
To see the Prosite summary for the hit, click on the PDOCxxxx number.

Hit from ScanProsite




Prosite pattern




Prosite Summary


Prosite Notes

 



To search for proteins with similar sequences, use:


 

Run a BLASTp search against the SwissProt database by pasting the protein sequence from GenScan into the input box on the Advanced BLAST page.  Choose the SwissProt database from the database listbox and the "blastp" program from the program listbox,
then press the "Submit" button. Format your results as "Flat query anchored with identities" and paste this alignment into your notebook.
 

BLASTP Alignment (against SwissProt)
BLASTP Alignment Notes

 


Conserved Domain


BLASTp Search also allows you to match your protein sequence to conserved protein domains in the Conserved Domain Database, generate a multiple sequence alignment based on this match, and explore 3D modeling templates for your sequence. Click on the Conserved domain displayed as "Specific hits" at the top of the BLASTp results page and again on the "Specific Hits" in the next page.

Conserve Domain Description

 

To obtain 3D Structure Template

To align your query protein to a similar sequence from a 3D structure, run the Protein BLAST (blastp) search and choose Search Set: Protein Data Bank proteins (pdb). Press the red "S" button beside the first hit (or any hit of interest). Click on the pink bar that represents the alignment in the graphic display, in the next page click on "Specific hits".   In the sequence alignment display, press the "View Structure and Alignment in Cn3D" button. This opens an interactive view of the sequence alignment and corresponding 3D structure in NCBI's Cn3D program. Locate the Prosite Motif you found earlier within the Cn3D alignment window by using View--Find Pattern. Zoom into the region, if necessary, by clicking in the sequence window and then by pressing z on your keyboard.  Highlight any nearby ligand by double clicking on it in the Strcutre window. Use Show Hide--Show selected residues from the Cn3D structure window to display the highlighted residues and ligand.

3D Structure Results

  

Other Tools for DNA and Protein Sequence Analysis