SlimShadey: A manipulation tool for multiple sequence alignments

Abstract

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 JavaFX 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.

Keywords: SlimShadey; manipulation; multiple sequence alignments; tool.

Figure 1

Processing of Caenorhabditis GLD-1 (defective in Germ Line Development) sequence alignment using SlimShadey. (A) Opal-aligned sequences homologous to Caenorhabditis elegans GLD-1 with >75% coverage obtained from WormBase release WS273 (https://wormbase.org/). (B) Shading of alignment from panel A. Base shading is BLOSUM62 gradient with green defined as a match to C. elegans and red defined as a mismatch to C. elegans, yellow is a custom regular expression highlighting (TP or SP, "[ST]-P"), Pfam (HMMER) defined KH domain (pink) and homodimerization domains (blue). (C) Bird's eye view of custom regular expression revealing clustering at N and C-terminal regions. (D) PNG output of complete alignment with all shading included. Arrows at the C-terminal end indicate the identification of motifs independent of position and the presence of gaps, respectively. (E) New tab (left) containing columns 39 to 60 of the original alignment, used to generate the sequence logo (right). Cel=C. elegans, Cre=C. remanei, Cla=C. latens, Cbre=C. brenneri, Cbr=C. briggsae, Cni=C. nigoni.