RESUMEN
Bioinformatics tools are essential for performing analyses in the omics sciences. Given the numerous experimental opportunities arising from advances in the field of omics and easier access to high-throughput sequencing platforms, these tools play a fundamental role in research projects. Despite the considerable progress made possible by the development of bioinformatics tools, some tools are tailored to specific analytical goals, leading to challenges for non-bioinformaticians who need to integrate the results of these specific tools into a customized pipeline. To solve this problem, we have developed the BioPipeline Creator, a user-friendly Java-based GUI that allows different software tools to be integrated into the repertoire while ensuring easy user interaction via an accessible graphical interface. Consisting of client and server software components, BioPipeline Creator provides an intuitive graphical interface that simplifies the use of various bioinformatics tools for users without advanced computer skills. It can run on less sophisticated devices or workstations, allowing users to keep their operating system without having to switch to another compatible system. The server is responsible for the processing tasks and can perform the analysis in the user's local or remote network structure. Compatible with the most important operating systems, available at https://github.com/allanverasce/bpc.git .
Asunto(s)
Biología Computacional , Programas Informáticos , Interfaz Usuario-Computador , Biología Computacional/métodos , Lenguajes de Programación , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , HumanosRESUMEN
The reduction in the cost of DNA sequencing and the total time to perform this process has resulted in a significant increase in the deposit of biological information in public databases such as the NCBI (National Center for Biotechnology Information). The production of large volumes of data per run has culminated in the need to develop algorithms capable of handling data with this new feature and assisting in analyses such as the assembly and annotation of prokaryotic genomes. Over the years, several pipelines and computational tools have been developed to automate this task and consequently reduce the total time to know the genetic content of a given organism, especially non-model organisms, collaborating with the identification of possible targets with biotechnological applicability. In the case of automatic annotation tools, the accuracy of the results is widely observed in the literature, however, this does not excludes the manual curation process, where the information inferred in the automatic process is verified and enriched by the curators. This task requires a time which is directly proportional to the number of gene products of the target organism under study. To assist in this process, we present the ReNoteWeb web tool, endowed with a simple and intuitive interface, to perform the assembly enhancement process, with the possibility of identifying the missing products in the original genomic sequence. In addition, ReNoteWeb is capable of performing the annotation process for all products, based on information obtained from highly accurate external databases. The engine responsible for performing the data processing was developed in JAVA and the web platform uses the resources of the Yii framework. The annotation produced by this platform aims to reduce the overall time in the manual curation process. Twenty-three organisms were used to validate the tool. The efficiency was verified by comparing the annotation of these same organisms available in the NCBI database and the annotation performed on the RAST platform. The tool is available at: http://biod.ufpa.br/renoteweb/.
Asunto(s)
Genoma , Genómica , Bases de Datos Genéticas , Genómica/métodos , Anotación de Secuencia Molecular , Análisis de Secuencia de ADN , Programas InformáticosRESUMEN
Genome annotation conceptually consists of inferring and assigning biological information to gene products. Over the years, numerous pipelines and computational tools have been developed aiming to automate this task and assist researchers in gaining knowledge about target genes of study. However, even with these technological advances, manual annotation or manual curation is necessary, where the information attributed to the gene products is verified and enriched. Despite being called the gold standard process for depositing data in a biological database, the task of manual curation requires significant time and effort from researchers who sometimes have to parse through numerous products in various public databases. To assist with this problem, we present CODON, a tool for manual curation of genomic data, capable of performing the prediction and annotation process. This software makes use of a finite state machine in the prediction process and automatically annotates products based on information obtained from the Uniprot database. CODON is equipped with a simple and intuitive graphic interface that assists on manual curation, enabling the user to decide about the analysis based on information as to identity, length of the alignment, and name of the organism in which the product obtained a match. Further, visual analysis of all matches found in the database is possible, impacting significantly in the curation task considering that the user has at his disposal all the information available for a given product. An analysis performed on eleven organisms was used to test the efficiency of this tool by comparing the results of prediction and annotation through CODON to ones from the NCBI and RAST platforms.
Asunto(s)
Bacterias/genética , Genómica/métodos , Anotación de Secuencia Molecular/métodos , Programas Informáticos , Bases de Datos Genéticas , Interfaz Usuario-ComputadorRESUMEN
The Next-Generation Sequencing (NGS) platforms provide a major approach to obtaining millions of short reads from samples. NGS has been used in a wide range of analyses, such as for determining genome sequences, analyzing evolutionary processes, identifying gene expression and resolving metagenomic analyses. Usually, the quality of NGS data impacts the final study conclusions. Moreover, quality assessment is generally considered the first step in data analyses to ensure the use of only reliable reads for further studies. In NGS platforms, the presence of duplicated reads (redundancy) that are usually introduced during library sequencing is a major issue. These might have a serious impact on research application, as redundancies in reads can lead to difficulties in subsequent analysis (e.g., de novo genome assembly). Herein, we present NGSReadsTreatment, a computational tool for the removal of duplicated reads in paired-end or single-end datasets. NGSReadsTreatment can handle reads from any platform with the same or different sequence lengths. Using the probabilistic structure Cuckoo Filter, the redundant reads are identified and removed by comparing the reads with themselves. Thus, no prerequisite is required beyond the set of reads. NGSReadsTreatment was compared with other redundancy removal tools in analyzing different sets of reads. The results demonstrated that NGSReadsTreatment was better than the other tools in both the amount of redundancies removed and the use of computational memory for all analyses performed. Available in https://sourceforge.net/projects/ngsreadstreatment/ .