The Clustal W algorithm is for gene level alignment of either protein or nucleotide sequences. To run a Clustal W alignment, select two or more sequences and choose Align > (Re)Align Using Clustal W.
If you wish to change method options, instead choose Align > Align with Options. The dialog has slightly different options, depending whether the sequences are protein or nucleotide (nucleotide shown below).
Change settings as desired:
- Use the Align drop-down menu to select sequences to align or realign.
- In the Using drop-down menu, choose Clustal W.
- Use the Scoring matrix drop-down menu to choose between these options:
| Matrix | Description | ||
|---|---|---|---|
| Nucleotide sequences only | |||
| IUB | The default scoring matrix used by BESTFIT for the comparison of nucleic acid sequences. X’s and N’s are treated as matches to any IUB ambiguity symbol. All matches score 1.9; all mismatches for IUB symbols score 0. | ||
| Clustal W | The previous system used by Clustal W, in which matches score 1 and mismatches score 0. All matches for IUB symbols also score 0. | ||
| Protein sequences only | |||
| BLOSUM | (Henikoff & Henikoff, 1992). BLOSUM is ideal for carrying out similarity searches. |
PAM | (Dayhoff et al., 1978). Widely used since the late 1970s. |
| GONNET | Derived from PAM matrices (Dayhoff et al., 1978) but more sensitive, and based on a much larger data set. | ||
| ID | Scores two identical amino acids as 1, and anything else as -10,000. | ||
- In the Iteration method drop-down menu, choose between None, All alignment steps, and Final alignment only. If you choose an item other than None, type the number of Maximum Iterations into the text box on the right.
- Enter the desired Multiple alignment parameters:
- Gap open penalty, the numerical penalty for introducing a gap of any length when calculating alignments. This penalty does not take into account the size of the gap. The default is 10.
- Gap extend penalty – This option affects the lengths of gaps, and must be zero or a negative number. Lowering the magnitude of the gap extension penalty may allow for longer gaps. The default is 0.20.
- Delay divergent sequences – This setting aligns more closely related sequences, delaying the alignment of more distantly related ones. Input the percent identity required to delay the addition of a sequence. The default is 30.
- Transition weight – This option is only available for nucleotide sequences and gives purine-purine or pyrimidine-pyrimidine substitutions (i.e., A-G or C-T) a weight between 0
and 1. One denotes a match, while zero denotes a mismatch. Assign a high score for closely related sequences and a lower score for distantly related ones. The default is 0.50.
- Gap open penalty, the numerical penalty for introducing a gap of any length when calculating alignments. This penalty does not take into account the size of the gap. The default is 10.
- Enter the desired Pairwise alignment parameters:
- Choose whether MegAlign Pro should use the Slow, accurate or Fast, approximate version of Clustal W when making the guide tree.
- Type in the Gap open penalty, the numerical penalty for introducing a gap of any length when calculating alignments. This penalty does not take into account the size of the gap. The default is 10.
- Gap extend penalty – This option affects the lengths of gaps, and must be zero or a negative number. Lowering the magnitude of the gap extension penalty may allow for longer gaps. The default is 0.1.
- Choose whether MegAlign Pro should use the Slow, accurate or Fast, approximate version of Clustal W when making the guide tree.
After making your changes:
- Choose Align to use the entered options to perform a multiple sequence alignment.
- Use the Reset to Default button if you would like to reset all values to the MegAlign Pro defaults.
- Select Cancel to leave the dialog without saving any changes or performing the alignment.
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