Instructions+for+amino+acid+sequencing

1. Click on the amino acid sequence comparison site called [|__LALIGN__]  hosted by the Swiss Institute of Bioinformatics.
 * T ****o compare two amino acid sequences**:

2. Scroll down to the green section and enter your first sequence title: “Normal LDL-Receptor AA sequence”.

3. Click on the [|__Normal LDL-receptor amino acid sequence__]  document on-line which has the single letter abbreviation code for the normal LDL-receptor. “Select and copy” the sequence. 4. Go back to the LALIGN page and paste the sequence into the “1st Query Sequence” box.

5. Go to the “Second sequence title” box and enter your title for the mutant LDL-receptor sequence.

6. Click on the [|__FH Mutant LDL-receptor amino acid sequence__]  document on-line which has the single letter abbreviation code for the FH mutant amino acid sequence. “Select and copy” the sequence.

7. When you have entered both titles and amino acid sequences, click “Run lalign”.

Below is an **example** of a comparison of four HIV virus mutants. (Scientists compare viral coat proteins that mutate or change from patient to patient to better understand its ability to infect its host.) Deleted amino acids are represented as a dash while the conserved or identical amino acids are aligned.
 * <span style="background-color: transparent; color: #000000; font-family: Arial; font-size: 15px; text-decoration: none; vertical-align: baseline;">How to read protein amino acid sequence results: **

<span style="background-color: transparent; color: #000000; font-family: Arial; font-size: 15px; text-decoration: none; vertical-align: baseline;">Use your data output from the LALIGN sequence comparison to answer the following questions. The amino acids are numbered and if they are identical they will have the same letter lined-up one over the other. Dashes represent gaps in the match up. ( <span style="background-color: transparent; color: #000000; font-family: Arial; font-size: 15px; vertical-align: baseline;">__Ignore__ <span style="background-color: transparent; color: #000000; font-family: Arial; font-size: 15px; text-decoration: none; vertical-align: baseline;"> the second and third sequence line-up in the LALIGN output.)