URL: http://athina.biol.uoa.gr/bioinformatics/NON-RED/index.html
Proper Citation: NON-RED (RRID:SCR_006225)
Description: A web tool to select biological sequences from a given set, with similarity / homology less than a user-defined level. This web-based application takes as input a set of N sequences and outputs a set of sequences of user-determined redundancy. Initially, the algorithm runs an all-against-all BLAST alignment on the input data set and creates an NxN matrix of pairwise distances defined by the similarity percentages. In the next step, the algorithm removes the sequence with the largest number of neighbors, causing that sequence not to be counted as a neighbor of any other sequence during the next iterations. It then reassesses the number of neighbors of each sequence and repeats the previous step until the sequences left over have no more neighbors. The user can specify the similarity (%) threshold and the minimum coverage length of the alignments. Sequences with a similarity below the threshold or a smaller coverage than the minimum length are not considered to be neighbors.
Abbreviations: NON-RED
Synonyms: NON-RED
Resource Type: data analysis service, production service resource, service resource, analysis service resource
Keywords: protein sequence, nucleotide, blast, algorithm, alignment, similarity, homology, sequence
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University of Athens Biophysics and Bioinformatics Laboratory |
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