SEDA
SEDA
SEDA (SEquence DAtaset builder) is an open source application for processing FASTA files containing DNA and protein sequences.
Features
Among other functions, SEDA allows you to:
- Filter sequences based on different criteria (including text patterns).
- Translate nucleic acid sequences into amino acid sequences.
- Execute BLAST analyses.
- Remove duplicated sequences.
- Sort, merge, split or reformat files.
- Perform gene annotation and run other third-party software (e.g. Clustal Omega).
For developers
Programmers can take advantage of the SEDA core to develop new operations to process FASTA files.
In addition, SEDA has a plugin-based architecture, so new functions can be added to the SEDA GUI through plugins.
For developers
Programmers can take advantage of the SEDA core to develop new operations to process FASTA files.
In addition, SEDA has a plugin-based architecture, so new functions can be added to the SEDA GUI through plugins.
Specifications
SEDA is a multi-platform application, this means that there are available distributions for Windows and GNU/Linux based operating systems.
SEDA is also open-source with license GPLv3.
Docker
A dockerized version of SEDA for Linux systems is available at Docker Hub.
In addition, the standalone version of SEDA can run the third-party dependencies using Docker images.
Docker
A dockerized version of SEDA for Linux systems is available at Docker Hub.
In addition, the standalone version of SEDA can run the third-party dependencies using Docker images.
Using SEDA? Please, cite these publications:
H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira; J. Vieira (2022) SEDA: a Desktop Tool Suite for FASTA Files Processing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 19(3), pp. 1850-1860. ISSN: 1545-5963
M. Reboiro-Jato; D. Pérez-Rodríguez; M. J. Da Silva Araujo; D. Vila-Fernández; C. Vieira; J. Vieira; H. López-Fernández (2024) SEDA 2024 Update: Enhancing the SEquence DAtaset Builder for Seamless Integration into Automated Data Analysis Pipelines. BMC Bioinformatics. Volume 25, article ID 200. ISSN: 1471-2105
Works using SEDA:
- H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) A bioinformatics protocol for quickly creating large-scale phylogenetic trees. 12th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2018. Toledo, Spain. 20 - June
- H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences. Interdisciplinary Sciences: Computational Life Sciences. ISSN: 1913-2751
- H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2019) Inferring Positive Selection in Large Viral Datasets. 13th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2019. Ávila, Spain. 26 - June
- D. Pérez-Rodríguez; M. Reboiro-Jato; C. P. Vieira; J. Vieira; H. López-Fernández (2024) Streamlining SEDA Pipelines with Compi: The Power of Convention over Configuration. 18th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2024. Salamanca, Spain. 26 - June