ArticleBioData mining2013
gff2sequence, a new user friendly tool for the generation of genomic sequences.
Article in BioData mining, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- Identification and structural characterization of pseudogenes in Fusarium graminearum.Scientific reports · 2025Article
- Genome-Wide Identification of Histone Modification Gene Families in the Model LegumePlants (Basel, Switzerland) · 2022Article
- Structural characterization and duplication modes of pseudogenes in plants.Scientific reports · 2021Article
- Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
- Gene Annotation Easy Viewer (GAEV): Integrating KEGG's Gene Function Annotations and Associated Molecular Pathways.F1000Research · 2018Article
- The Evolutionary Basis of Translational Accuracy in Plants.G3 (Bethesda, Md.) · 2017Article
- Sequence Polymorphisms and Structural Variations among Four Grapevine (Frontiers in plant science · 2017Article
- Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen.BMC genomics · 2016Article
- Altools: a user friendly NGS data analyser.Biology direct · 2016Article
- New insights into the interplay between codon bias determinants in plants.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGeneral Feature Format (GFF) files are used to store genome features such as genes, exons, introns, primary transcripts etc. Although many software packages (i.e. ab initio gene prediction programs) can annotate features by using such a standard, a small number of tools have been developed to extract the corresponding sequence information from the original genome. However the present tools do not execute either a quality control or a customizable filter of the annotated features is available.
findingsgff2sequence is a program that extracts nucleotide/protein sequences from a genomic multifasta by using the information provided by a general feature format file. While a graphical user interface makes this software very easy to use, a C++ algorithm allows high performance together with low hardware demand. The software also allows the extraction of the genic portions such as the untranslated and the coding sequences. Moreover a highly customizable quality control pipeline can be used to deal with anomalous splicing sites, incorrect open reading frames and not canonical characters within the retrieved sequences.
conclusionsgff2sequence is a user friendly program that allows the generation of highly customizable sequence datasets by processing a general feature format file. The presence of a wide range of quality filters makes this tool also suitable for refining the ab initio gene predictions.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.