BALCONY: an R package for MSA and functional compartments of protein variability analysis
| Autor: | Maria Bzówka, Artur Góra, Michał Stolarczyk, Alicja Płuciennik, Tomasz Magdziarz, Agata Raczyńska |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Computer science Entropy Conservation/entropy analysis lcsh:Computer applications to medicine. Medical informatics medicine.disease_cause computer.software_genre Biochemistry Evolution Molecular 03 medical and health sciences 0302 clinical medicine Protein structure Structural Biology MSA medicine Humans Amino Acid Sequence lcsh:QH301-705.5 Molecular Biology Mutation Applied Mathematics R package Proteins A protein Protein engineering Protein superfamily Computer Science Applications Visualization 030104 developmental biology lcsh:Biology (General) lcsh:R858-859.7 Protein evolution Data mining DNA microarray Sequence Alignment computer Software 030217 neurology & neurosurgery |
| Zdroj: | BMC Bioinformatics BMC Bioinformatics, Vol 19, Iss 1, Pp 1-8 (2018) |
| ISSN: | 1471-2105 |
| Popis: | Background Here, we present an R package for entropy/variability analysis that facilitates prompt and convenient data extraction, manipulation and visualization of protein features from multiple sequence alignments. BALCONY can work with residues dispersed across a protein sequence and map them on the corresponding alignment of homologous protein sequences. Additionally, it provides several entropy and variability scores that indicate the conservation of each residue. Results Our package allows the user to visualize evolutionary variability by locating the positions most likely to vary and to assess mutation candidates in protein engineering. Conclusion In comparison to other R packages BALCONY allows conservation/variability analysis in context of protein structure with linkage of the appropriate metrics with physicochemical features of user choice. Availability: CRAN project page: https://cran.r-project.org/package=BALCONY and our website: http://www.tunnelinggroup.pl/software/ for major platforms: Linux/Unix, Windows and Mac OS X. Electronic supplementary material The online version of this article (10.1186/s12859-018-2294-z) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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