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SigniSite 2.0 Server

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SigniSite 2.0 identifies amino acid residues, which in a FASTA multiple alignment are found to be significantly associated with the phenotype of the data set. The phenotype is represented by a continuous numerical parameter placed last in the identifier of each sequence. For test of server functionality, please see 'Sample data'.

Instructions Output format Article abstract

Submission

Sample data
Please note that non-amino acid residue characters, will not be included in the evaluation,
i.e. anything other than 'ARNDCQEGHILKMFPSTWYV' will be excluded.		 Sample data for test of server functionality is available. The sample data will reproduce the results used on 'output format' page.
To load the sample data, simply click the 'Load sample data' button below and 'submit':
Paste a multiple alignment in FASTA format into the field below:
SigniSite_logo
Submit a multiple alignment file in FASTA format directly from your local disk:

HIVdb benchmark data set
Please click here to download. Please cite:
- Soo-Yon Rhee, Matthew J. Gonzales, Rami Kantor, Bradley J. Betts, Jaideep Ravela, and Robert W. Shafer (2003) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research, 31(1), 298-303.
- Shafer RW(2006). Rationale and Uses of a Public HIV Drug-Resistance Database. Journal of Infectious Diseases 194 Suppl 1:S51-8

Options

Instructions on the meaning of the parameters below, can be found here
Significance threshold α =
Method for correction for multiple testing
Choose sorting of numerical values
Unique sequence ID for relative numbering
Type of logo
Please click here for instructions
Should gaps be ignored? By default SigniSite-2.0 consideres gaps as amino acid residue #21

Reference / citation / citing SigniSite

For publication of results, please cite:

SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments
Leon Eyrich Jessen, Ilka Hoof, Ole Lund, and Morten Nielsen
Nucl. Acids Res. first published online June 12, 2013 doi:10.1093/nar/gkt497

Abstract or Open Access Full Text (PDF)



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This file was last modified Thursday 13th 2013f June 2013 10:24:06 GMT