Task 2: Sequence alignments (sequence searches and multiple alignments)

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Revision as of 17:10, 23 May 2011 by Pfeiffenberger (talk | contribs) (Methodology)

Task description

The full description of this task can be found here.

Task 2.1: Sequence searches

Task 2.2: Multiple sequence alignments


For each identity range (99%-90%, 89%-60, 59%-40% and 39%-20%) we selected five sequences of which at least one sequence has a solved structure as well. In order to find these sequences we looked in our blast and psi-blast results for appropriate sequences, four for each identity range. A sequences was considered as appropriate if it has the wanted sequence identity to our reference sequence and if this sequence has roughly the same length as our reference sequence. The reason for this is that we wanted to avoid leading and trailing gaps in our alignments. However, this was not always possible , especially for the low identity range (39%-20%). Last but not least, we used our hhsearch results (which was queried against a profile database of all pdb entries) to find appropriate sequences for each identity range. The list of selected sequences is as follows:

Sequence Identity GI/PDB Remark
row 1, cell 1 row 1, cell 2 row 1, cell 3
row 2, cell 1 row 2, cell 2 row 2, cell 3
row 3, cell 1 row 3, cell 2 row 3, cell 3