Abstract:SNUFER is software for the automatic localization and generation of tables used for the presentation of single nucleotide polymorphisms (SNPs). A multiple sequence alignment is generated using ClustalW ran inside SNUFER using an input of a FASTA file containing the sequences to be analyzed. The ClustalW output file is then used to generate a table which displays the SNPs detected in the aligned sequences and their degree of similarity. This table can be exported to Microsoft Word, Microsoft Excel or as a single text file, permitting further editing for publication. The software was written using Delphi 7 for programming and FireBird 2.0 for sequence database management. It is freely available for non-commercial use and can be downloaded from the URL http://www.heranza.com.br/bioinformatica2.htm.Keywords: software; single nucleotide polymorphisms; multiple sequence alignment; ClustalW Background:In pathogenic microorganisms, single nucleotide polymorphisms (SNP) are used to define strains and are analyzed for possible correlations with geographic origin and differences in pathogenesis [1, 2]. After DNA sequencing of gene fragments from different individuals of the same species, SNPs are identified by multiple alignment of DNA sequences. One of the most popular software used for this purpose is Clustal, which employs a fast pairwise alignment algorithm [3], helping the user to identify identical and non-identical nucleotides along sequences. The most popular way of presenting SNPs based on these results is to manually build a table which shows the nucleotide changes between a selected reference sequence and the other aligned sequences. SNUFER was developed to automatize this task by integrating the steps of multiple sequence alignment, SNP identification and data presentation in a publication format.
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