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- KAlign - the algorithm, provided by the Kalign tool (integrated as an External Tool, check the Data Analysis Tools page for details). This tool uses the Wu-Manber string-matching algorithm. The algorithm details are described in the corresponding publication [Lassmann T, Sonnhammer EL. Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics. 2005 Dec 12;6:298. doi: 10.1186/1471-2105-6-298. PMID: 16343337; PMCID: PMC1325270 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1325270/].
The 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 Terminal 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 same algorithm, which is used for the Smith-Waterman Search (check the page for the algorithm details - the alignment process works in a same way as the searching process).
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 SSE2.
- Scoring matrix - scoring matrix.
- Gap open penalty - penalty for opening a gap.
- Gap extension penalty — penalty for extending a gap.
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