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SigniSite 2.1 Server: Residue level genotype phenotype correlation in protein multiple sequence alignments

Server Introduction
SigniSite performs residue level genotype phenotype correlation in protein multiple sequence alignments by identifying amino acid residues significantly associated with the phenotype of the data set. Input is a protein multiple sequence alignment in FASTA format. The phenotype is represented by a real-valued numerical parameter placed white-space separated, last in the identifier of each sequence (example). For test of server functionality, please see 'Sample data' below the SigniSite logo.

We care about our users and any feedback is very welcome!
Please send any question and/or comments to us, by writing to:

New November 2018: Server Functional
The issue with aligning sequences have been solved and SigniSite is up and running again.
August 2016: Server functional
SigniSite is now up and running again after technical downtime.
August 2016: Update
SigniSite was moved to a new server.
February 2014: Added output
In order to aid users in locating the residue with the strongest phenotypic association, a rank list is available for download, after submission and evaluation. Please see output format for further elaboration.

Instructions Output format Article abstract Download Benchmark Dataset


Please note that SigniSite will only accept characters corresponding to the 20 proteogenic amino acid residues and gaps, i.e. anything other than 'ARNDCQEGHILKMFPSTWYV-' will result in an error message.

Paste a multiple alignment in FASTA format into the field below:

Submit a multiple alignment file in FASTA format directly from your local disk:

Sample data

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'

HIVdb benchmark data set

Click here to download. Please note that the benchmark data set was compiled from the Stanford University HIV drug resistance database, see "How to Cite the HIV Drug Resistance Database".


Instructions on the meaning of the parameters below, can be found here
Exclude gaps from the evaluation
Significance threshold α =
Method for correction for multiple testing
Choose sorting of numerical values
Unique sequence ID for relative numbering
Type of logo
Include all positions in logo
Logo plot title, use quotes and underscore, e.g.: "My_Title"
Please click here for instructions


For security reasons, there is a restriction on maximum 500,000 amino acid residues in the submitted multiple sequence aligment. Should you wish to submit an alignment larger than this, please write us at

Reference / citation / citing SigniSite

For publication of results, please cite [1]
  1. Jessen LE, Hoof I, Lund O, Nielsen M.
    SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.
    Nucleic Acids Res. 2013 Jul;41(Web Server issue):W286-91. doi: 10.1093/nar/gkt497. Epub 2013 Jun 12.


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