Does Jalview work with nucleotide sequences and alignments?


Thank you to everyone who wrote letters of support last year for our application to the BBSRC, we should hear the outcome in the next couple of months.

We are now applying to the Wellcome Trust to renew funding to support Jalview's use in biomedical sequence analysis, including interpretation of genomic variation and long read RNA data (e.g. Nanopore) at the protein coding level. If you would like Jalview to continue to develop and be supported then please take a few minutes to write us a support letter saying how you use Jalview in your research/teaching.

Write as a PDF including your institution's heading and send to:
support_jalview@bartongroup.org by Friday 22nd March 2019.

Thank you!

Versions of Jalview released before November 2012 did not include any special support for scoring or visualizing nucleotide sequences, although they could read, write and manipulate DNA and RNA sequences, and calculate a consensus.

Version 2.8 of Jalview was the first release to include special support for nucleic acid sequences, and included a substitution matrix that copes with both RNA and DNA symbols which can be used to calculate trees and principal component analysis plots from alignments. Nucleotide base pair patterns provided as WUSS or VIENNA dot-bracket annotation can also be visualised, and used to calculate base-pair consensus score and sequence logos. Version 2.8 of the Jalview Desktop also included VARNA for interactive exploration of 2D RNA structure. For the latest information about nucleic acid support, see the nucleic acid section of Jalview's help pages.  

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