@*~RSC_HELP_TUTORIAL_ALIG_ALIGNMENTS

Introduction

This tutorial shows how two alignments can be combined to one alignment. As example some WIKI:Proteasome subunits are loaded: HTMLDOC_BUTTON:SBUT_TUTORIAL_LOAD_EXAMPLE_AA! These subunits belong to two different classes: Bacterial subunits start with "hs_" and eukaryotic alpha 2 with "a2_". You can align all sequences using the tool-button HTMLDOC_BUTTON:SBUT_ALIGN! or the dialog HTMLDOC_BUTTON:BUT_C1(DialogAlign)!. The sequence alignment algorithms work well for sequence of the same group but fail to align bacterial with eukaryotic subunits because the sequences are very dissimilar.

Aligning all bacterial sequences

Align all bacterial sequences (names starting with "hs_") choosing a sequence based method such as HTMLDOC_COMBO_CLASS:BUT_C1(ClustalW). If the sequence names can be recognized by a string pattern ( in our example the names start with "hs_"), the selection can be performed with the tool-button HTMLDOC_ICON:IC_SEARCH.

Stack all bacterial sequences in one line

Use the dialog HTMLDOC_BUTTON:SBUT_MANY1ROW_DIA! to place all aligned bacterial sequences into one row such that hs_EscherichiaColi.pdb stays on top. This is important because hs_EscherichiaColi.pdb is the one with c-alpha coordinates. As a result all bacterial sequences but hs_EscherichiaColi.pdb vanish. The number 4 in the row header indicates the number of sequences in that row. All gaps inserted into hs_EscherichiaColi.pdb will simultaneously also be inserted into the 4 sequences.

Aligning all eukaryotic sequences

Proceed in the same way with the eukaryotic sequences.

Align both blocks three-dimensionally

In the alignment pane only two sequences are currently shown: hs_EscherichiaColi.pdb and a2_SaccharomycesCerevisiae.dssp. Though their sequences are very different, their 3D-structures look similar as can be seen by superimposing the structures in the backbone 3D view: HTMLDOC_BUTTON:SBUT_3D!. Align both rows.

Place each Sequence in a row of its own

Separating the stacked sequences is also performed in the dialog HTMLDOC_BUTTON:SBUT_MANY1ROW_DIA!. Select hs_EscherichiaColi.pdb and press the button and then select a2_SaccharomycesCerevisiae.dssp and press the button. As a all sequences are visible in the multiple alignment. *@