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FA

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Grant support

The research leading to these results has received funding from the Plataforma de Recursos Biomoleculares y Bioinformaticos PT 13/0001/0021 from ISCIII, a platform co-funded by the European Regional Development Fund (FEDER) and from the Plan Estatal project funded under grant number PGC2018-094017-B-I00 from the Spanish Ministry of Science and Innovation (AEI/FEDER). We acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the CERCA Programme/Generalitat de Catalunya.

Analysis of institutional authors

Pulido, ThCorresponding AuthorCamara, FAuthorPonomarenko, JAuthorGuigo, RAuthor

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Article

FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow

Publicated to:Genes. 12 (10): 1645- - 2021-10-01 12(10), DOI: 10.3390/genes12101645

Authors: Vlasova, A; Pulido, TH; Camara, F; Ponomarenko, J; Guigo, R

Affiliations

Abstract

Functional annotation allows adding biologically relevant information to predicted features in genomic sequences, and it is, therefore, an important procedure of any de novo genome sequencing project. It is also useful for proofreading and improving gene structural annotation. Here, we introduce FA-nf, a pipeline implemented in Nextflow, a versatile computational workflow management engine. The pipeline integrates different annotation approaches, such as NCBI BLAST+, DIAMOND, InterProScan, and KEGG. It starts from a protein sequence FASTA file and, optionally, a structural annotation file in GFF format, and produces several files, such as GO assignments, output summaries of the abovementioned programs and final annotation reports. The pipeline can be broken easily into smaller processes for the purpose of parallelization and easily deployed in a Linux computational environment, thanks to software containerization, thus helping to ensure full reproducibility.

Keywords

containerizationfunctional annotationpipelineBioinformaticsContainerizationDatabaseFunctional annotationGene ontologyGenomesIdentificationPathwaysPipelinePlatformReconstructionReproducibility

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Genes due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2021, it was in position 72/175, thus managing to position itself as a Q2 (Segundo Cuartil), in the category Genetics & Heredity. Notably, the journal is positioned en el Cuartil Q2 para la agencia Scopus (SJR) en la categoría Genetics.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2025-06-03:

  • WoS: 3
  • Scopus: 3
  • Europe PMC: 3
  • OpenCitations: 3

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-06-03:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 31.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 31 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 8.2.
  • The number of mentions on the social network X (formerly Twitter): 13 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: Last Author (GUIGÓ SERRA, RODERIC).

the author responsible for correspondence tasks has been HERMOSO PULIDO, ANTONIO.