Child pages
  • Pairwise Alignment
Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 2 Current »

To align two sequences go to the Pairwise Alignment tab of the Options Panel:



Select two sequence from the original alignment, select the parameters and click on the Align button. The following parameters are available:

Algorithm - algorithm of the pairwise alignment. There are two algorithms:

Hirschberg (KAlign) - algorithm has the following parameters:

Gap open penalty - indicates the penalty applied for opening a gap. The penalty must be negative.

Gap extension penalty - indicates the penalty applied for extending a gap.

Terminate gap penalty - the penalty to extend gaps from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences.

Bonus score - a bonus score that is added to each pair of aligned residues.

Smith-Waterman - the following parameters are available:

Algorithm version - version of the algorithm implementation. Non-classic versions produce the same results as classic but much faster. To use these optimizations our system must support these capabilities: OPENCL, SSE2 or SW_classic.

Scoring matrix - scoring matrix.

Gap open penalty - penalty for opening a gap.

Gap extension penalty — penalty for extending a gap.

Output settings - settings of the otput file.

 

  • No labels