Clustal

Clustal is a widely used computer program for Multiple Sequence Alignment. The current version is 2.1. There are two versions of the program:

  • ClustalW: a command line program
  • ClustalX: a graphical user interface. The program is available for Windows, Mac OS and Unix / Linux.

Input / output

The program can process a wide range of input formats, including NBRF / PIR, FASTA, EMBL / SwissProt and UniProt, Clustal, GCC / MSF, RSF GCG9 and GDE.

The output can be in the following formats: Clustal, NBRF / PIR, GCG / MSF, PHYLIP, GDE, NEXUS.

Multiple sequence alignment

Clustal performs three main steps:

These steps are performed automatically when you Do Complete Alignment ( Complete alignment ) perform selects. Other options include Do Alignment from guide tree ( Make reference to an alignment guide tree ) and Produce guide tree only ( Only the Guide Tree create ).

Profile alignments

Pairwise alignments are calculated for all and against all sequences; Matches are stored in a matrix. This is then placed in a distance matrix ( distance matrix) converted, where the distance value reflects the evolutionary distance between each pair of sequences.

From this distance matrix is calculated by the neighbor-joining algorithm for clustering ( Neighbor -joining clustering algorithm ) a guide tree or a phylogenetic tree constructed that determines the sequence aligns in the sequence pairs ( arranged ) and will be combined with previous alignments. Sequences aligns progressively each branch point, starting with that sequence pair having the smallest distance.

Settings

Users can using the default sequences alignieren, but from case to case, it is advisable to use your own parameters.

The main parameters are gap opening penalty and gap extension penalty (see sequence alignment ).

Accelerated version

An FPGA -based version of ClustalW algorithm is offered by the company Progeniq and recorded a twenty- fold increase in processing speed compared to the software implementation.

Swell

  • J. D. Thompson et al. (1997): The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. In: Nucleic Acids Research. Vol 25, pp. 4876-4882. PMID 9396791
  • R. Chenna et al. (2003): Multiple sequence alignment with the Clustal series of programs. In: Nucleic Acid Research. Vol 31, pp. 3497-3500. PMID 12824352
  • M. A. Larkin et al. (2007) Clustal W and Clustal X version 2.0. In: Bioinformatics. Vol 23, pp. 2947-2948. PMID 17846036
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