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Slim Shadey: A manipulation tool for multiple sequence alignments



Avi Shah, Aneesha Kodati & Sudhir Nayak*



The College of New Jersey, 2000 Pennington Rd., Ewing, NJ, USA 08628-0718; *Corresponding author



Aneesha Kodati E-mail: aneesha.kodati@gmail.com

Sudhir Nayak E-mail: nayak@tcnj.edu

Avi Shah E-mail: shaha65@tcnj.edu


Article Type

Research Article



Received May 1, 2023; Revised May 31, 2023; Accepted May 31, 2023, Published May 31, 2023



The visualization of sequence alignments with the addition of meaningful shading and annotation is critical to convey the importance of structural elements, domains, motifs, and individual residues. Hence, we have developed a Java FX based software package (SlimShadey) with an intuitive graphical user interface that allows for the creation and visualization of features on sequence alignments, as well as trimming and editing of subsequences. SlimShadey will run without modification on Windows 7 (or higher) and will also run on OS X / macOS, most Linux distributions, and servers.  SlimShadey features real-time shading and comparison of residues based on user-defined measures of conservation such as frequency, user-selected substitution matrices, composition-based consensus sequence, regular expressions, and hidden Markov models. The software also allows users to generate custom sequence logos, configurable publication quality images of alignments with shading and annotation, and shareable self-contained project files for collaboration.  SlimShadey is an open source freely available Java program. Compiled .jar executables, source code, supplementary materials including the user manual, links to video tutorials, and all sample data are available through the URLS at availability.



SlimShadey, manipulation, tool, multiple sequence alignments



Shah et al. Bioinformation 19(5): 659-662 (2023)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.