CLANS Displays pairwise similarities for fasta format sequences
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BLAST similarity fasta sequence fasta sequence similarity BLAST search

CLANS Description

Displays pairwise similarities for fasta format sequences CLANS is a free software that takes unaligned fasta format sequences a input, performs all-against-all BLAST searches and displays the pairwise similarities in either 2D or 3D graphs. Contrary to phylogenetic inference methods this approach uses unaligned sequences and works better the more sequences are provided as an increase in number of pairwise similarities better averages out the chance hits that plague standard BLAST comparisons.While for protein data the knowledge of "homology" generally helps in formulating a hypothesis, as , most likely, some functional annotation will be available for at least some of the close or more distant homologs, the knowledge of apparent co-expression helps a lot less for microarray data. This due to two problems. First of all there is the huge amount of genes present on the microarray chip and the, generally, low number of experiments and/or replicates that are performed. The probability of two genes showing co-expression, even though they are not causally related in any way, is relatively high. The second is that knowing that a group of genes co-express does not help without having at least an inkling of what some of them do. Therefore we need to include additional data such as functional annotation, cellular localization or pathway information. Requirements: · Java 1.5 or later

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