Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper.
Bioinformatics
; 40(5)2024 May 02.
Article
em En
| MEDLINE
| ID: mdl-38648741
ABSTRACT
SUMMARY:
SIMSApiper is a Nextflow pipeline that creates reliable, structure-informed MSAs of thousands of protein sequences faster than standard structure-based alignment methods. Structural information can be provided by the user or collected by the pipeline from online resources. Parallelization with sequence identity-based subsets can be activated to significantly speed up the alignment process. Finally, the number of gaps in the final alignment can be reduced by leveraging the position of conserved secondary structure elements. AVAILABILITY AND IMPLEMENTATION The pipeline is implemented using Nextflow, Python3, and Bash. It is publicly available on github.com/Bio2Byte/simsapiper.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Proteínas
/
Alinhamento de Sequência
/
Análise de Sequência de Proteína
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
Bélgica