Introduction

Amino acid sequences change during evolution and remote homologs are difficult to align. Here is a list of some techniques in STRAP to solve this problem.

Dotplot

A WIKI:Dot_plot_(bioinformatics) of both proteins is helpful in many cases: BUTTON:DialogDotPlot!. In the dot-plot-pane you can often identify a diagonal trace which is formed by pairs of similar residues. You can set marks on this trace. A mark in the dot-plot-pane corresponds to one residue in either protein. The corresponding residue positions in both proteins are highlighted in the alignment. You can insert gaps until they are above each other in the alignment pane.

Highlight patterns

Sometimes it is helpful to highlight search strings in the alignment. BUTTON:DialogHighlightPattern!. See WIKI:Sequence_motif

Find homologous structures

Try to find proteins in the pdb that are closely related to your two proteins BUTTON:DialogBlast!.

WIKI:Structural_alignment

The C-alpha atoms of two protein
structures can be superimposed. BUTTON:DialogSuperimpose3D!.

Highlight spatially equivalent residues

After superposition of all homolgous proteins it makes sense to highlight structurally equivalent residues. Imagine a sphere around the C-alpha atom of the residue where the alignment cursor is. All amino acids with C-alpha atoms within this sphere are highlighted. This involves the dialog BUTTON:DialogSelectionOfResiduesMain! and the method COMBO:Distance3DToCursor. See Tutorial "superimpose proteins ..." for details.

Intermediate sequences

The alignment of some sequences becomes easier when further homologous sequences are included into the alignment. Therefore common relatives can be identified using BLAST search BUTTON:IntermediateSeq!.