ExPASy, or Expert Protein Analysis System, is a resource that was developed as part of the Swiss Insitute of Bioinformatics (SIB). The site offers many options for sequence alignment, including: ClustalW, MUSCLE, and T.Coffee. This article will focus on using ClustalW, which is a program designed for multiple sequence alignment of nucleic acid and protein sequences (Figure 1). This is a useful tool for looking at relationships, including that of a particular gene among different species, or comparing two different genes. Up to 30 FASTA-formatted sequences can be submitted at a time. If only two sequences are being analyzed, a pairwise alignment can be preformed. FASTA format is a text-based way of representing nucleotide or peptide sequences. FASTA originated from a software package, but is now commonly used for Bioinformatics. DNA sequences can be obtained through GenBank, which is a genetic sequence database generated by the NIH. Genbank includes all DNA sequences that are publically available.
An example of an article that uses ExPASy: Buel et al. (cited in the references section).
How to use the databaseEditOnce in the ClustalW site, FASTA-formatted sequences for multiple genes and species can be added for an alignment, as shown in Figure 2 . For each FASTA file, the first line (circled in blue in Figure 3) gives the gene infomation. The following line starts the sequence. Figure 4 shows an expample of a multiple sequence alignment. *'s indicate identical sequences.
Buel GR, Rush J, Ballif BA (2010) Fyn promotes phosphorylation of collapsin mediator protein 1 at tyrosine 504, a novel, isoform-specific regulatory site. J Cell Biochem 111(1): 20-28.
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