PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities.
Bioinformatics
; 35(24): 5313-5314, 2019 12 15.
Article
en En
| MEDLINE
| ID: mdl-31318409
ABSTRACT
SUMMARY:
Identification of the amino-acid motifs in proteins that are targeted for post-translational modifications (PTMs) is of great importance in understanding regulatory networks. Information about targeted motifs can be derived from mass spectrometry data that identify peptides containing specific PTMs such as phosphorylation, ubiquitylation and acetylation. Comparison of input data against a standardized 'background' set allows identification of over- and under-represented amino acids surrounding the modified site. Conventionally, calculation of targeted motifs assumes a random background distribution of amino acids surrounding the modified position. However, we show that probabilities of amino acids depend on (i) the type of the modification and (ii) their positions relative to the modified site. Thus, software that identifies such over- and under-represented amino acids should make appropriate adjustments for these effects. Here we present a new program, PTM-Logo, that generates representations of these amino acid preferences ('logos') based on position-specific amino-acid probability backgrounds calculated either from user-input data or curated databases. AVAILABILITY AND IMPLEMENTATION PTM-Logo is freely available online at http//sysbio.chula.ac.th/PTMLogo/ or https//hpcwebapps.cit.nih.gov/PTMLogo/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Procesamiento Proteico-Postraduccional
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Bioinformatics
Año:
2019
Tipo del documento:
Article
País de afiliación:
Tailandia