• SlimShadey: A manipulation too...

*Result*: SlimShadey: A manipulation tool for multiple sequence alignments.

Title:
SlimShadey: A manipulation tool for multiple sequence alignments.
Authors:
Shah A; The College of New Jersey, 2000 Pennington Rd., Ewing, NJ, USA 08628-0718., Aneesha K; The College of New Jersey, 2000 Pennington Rd., Ewing, NJ, USA 08628-0718., Sudhir N; The College of New Jersey, 2000 Pennington Rd., Ewing, NJ, USA 08628-0718.
Source:
Bioinformation [Bioinformation] 2023 May 31; Vol. 19 (5), pp. 659-662. Date of Electronic Publication: 2023 May 31 (Print Publication: 2023).
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Biomedical Informatics Pub. Group Country of Publication: Singapore NLM ID: 101258255 Publication Model: eCollection Cited Medium: Print ISSN: 0973-2063 (Print) Linking ISSN: 09732063 NLM ISO Abbreviation: Bioinformation Subsets: PubMed not MEDLINE
Imprint Name(s):
Original Publication: [Singapore] : Biomedical Informatics Pub. Group, 2005-
References:
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549. (PMID: 29722887)
Bioinformatics. 2007 Nov 1;23(21):2947-8. (PMID: 17846036)
Protein Eng. 1993 Jan;6(1):37-40. (PMID: 8433969)
Trends Biochem Sci. 1995 Sep;20(9):374. (PMID: 7482707)
Bioinformatics. 2007 Jul 1;23(13):i559-68. (PMID: 17646343)
Bioinformatics. 1998;14(9):821-2. (PMID: 9918955)
Nucleic Acids Res. 2018 Jul 2;46(W1):W200-W204. (PMID: 29905871)
Bioinformatics. 2009 May 1;25(9):1189-91. (PMID: 19151095)
Nucleic Acids Res. 1990 Oct 25;18(20):6097-100. (PMID: 2172928)
Bioinformatics. 1998;14(4):380-1. (PMID: 9632837)
Biotechniques. 2000 Jun;28(6):1102, 1104. (PMID: 10868275)
J Mol Biol. 1987 Jun 20;195(4):957-61. (PMID: 3656439)
Contributed Indexing:
Keywords: SlimShadey; manipulation; multiple sequence alignments; tool
Entry Date(s):
Date Created: 20231027 Latest Revision: 20241001
Update Code:
20260130
PubMed Central ID:
PMC10599665
DOI:
10.6026/97320630019659
PMID:
37886161
Database:
MEDLINE

*Further Information*

*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.
(© 2023 Biomedical Informatics.)*