7.1 Color alignment

OPTIONAL TASK
Create a colored version similar to the Walls paper following instructions below. This is done in 2 steps:

1- Optional: remove the PDB sequences to better match the Walls paper. See command below.
2- Go to the ESPript server: http://espript.ibcp.fr to create output.

The results obtained from our TCoffee alignment can also be converted to this nice rendering and we can additionally include protein structure information in the final output.

7.1.1 Remove PDB sequences (optional)

In order to better match the Walls paper, we’ll remove the PDB files that were added before converting to this format. To accomplish this we can use the command below.

fgrep -v 6VXX sarbecos.aln | \
fgrep -v 6VYB | fgrep -v 2AJF | \
fgrep -v 6LZG > sarbecos-4.aln

Command Design info:

The .aln format is simple and we can simply remove the lines containing the code of the PDB sequences. The fgrep will recognize these lines and the flag -v will ask to remove them. The result of the first command is “piped” into the next until all removals are satisfied. The final output is redirected into a file.

Note: Alternate methods could be used, for example using egrep to remove two patterns at the same time: egrep -v "6VXX|6VYB" sarbecos.aln | egrep -v "2AJF|6LZG". Other solutions can use awk (e.g. awk '!/6VXX/' sarbecos.aln etc.)

7.1.2 Create colored output

Within the ESPript server:

use alignment file sarbecos-4.aln
provide a PDB structure code for structure annotation (6VYB)
specify chain A