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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
Published on: March 22, 2018
gff2sequence, a new user friendly tool for the generation of genomic sequences
Salvatore Camiolo1, Andrea Porceddu
1Dipartimento di Agraria, Università degli Studi di Sassari, Sassari 07100, Italy. s.camiolo@uniss.it.
Biodata Mining
|September 12, 2013
Summary
gff2sequence is a new program that extracts genome sequences using General Feature Format (GFF) files. It offers customizable quality control for refining gene predictions and generating sequence datasets.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- General Feature Format (GFF) files are standard for annotating genome features.
- Existing tools lack quality control and customizable filtering for extracted sequences.
- Ab initio gene prediction programs generate annotations but require sequence extraction tools.
Purpose of the Study:
- To develop a user-friendly program for extracting nucleotide and protein sequences from genomic data using GFF files.
- To implement customizable quality control features for refining extracted sequences.
- To provide a tool for enhancing the accuracy of gene predictions.
Main Methods:
- Developed gff2sequence, a C++ program with a graphical user interface.
- Implemented sequence extraction for nucleotide and protein formats.
- Integrated a customizable quality control pipeline for filtering sequences.
- Enabled extraction of specific genic portions like coding and untranslated sequences.
Main Results:
- gff2sequence efficiently extracts sequences from multifasta genomes based on GFF annotations.
- The software provides a user-friendly interface and high performance with low hardware requirements.
- Customizable filters address issues like anomalous splicing sites, incorrect open reading frames, and non-canonical characters.
- The tool facilitates the generation of tailored sequence datasets.
Conclusions:
- gff2sequence is an easy-to-use program for creating customizable sequence datasets from GFF files.
- Its comprehensive quality filters enhance its utility for refining ab initio gene predictions.
- The program offers a valuable solution for sequence extraction and quality control in genomics research.
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