ArticleBioinformatics (Oxford, England)2014
MFCompress: a compression tool for FASTA and multi-FASTA data.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections.GigaScience · 2026Article
- A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules.Briefings in functional genomics · 2025Article
- OReO: optimizing read order for practical compression.Bioinformatics advances · 2025Article
- JARVIS3: an efficient encoder for genomic data.Bioinformatics (Oxford, England) · 2024Article
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- Image-centric compression of protein structures improves space savings.BMC bioinformatics · 2023Article
- Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format.Patterns (New York, N.Y.) · 2022Review
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- FASTAFS: file system virtualisation of random access compressed FASTA files.BMC bioinformatics · 2021Article
- Disk compression of k-mer sets.Algorithms for molecular biology : AMB · 2021Article
- Representation ofJournal of computational biology : a journal of computational molecular cell biology · 2021Article
- The Tip Region on VP2 Protein of Bluetongue Virus Contains Potential IL-4-Inducing Amino Acid Peptide Segments.Pathogens (Basel, Switzerland) · 2020Article
- Efficient DNA sequence compression with neural networks.GigaScience · 2020Article
- Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences.GigaScience · 2020Article
- Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements.GigaScience · 2020Article
- Human mitochondrial genome compression using machine learning techniques.Human genomics · 2019Article
- Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences.Bioinformatics (Oxford, England) · 2019Article
- Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application.Briefings in bioinformatics · 2019Review
- MZPAQ: a FASTQ data compression tool.Source code for biology and medicine · 2019Article
- HRCM: An Efficient Hybrid Referential Compression Method for Genomic Big Data.BioMed research international · 2019Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationThe data deluge phenomenon is becoming a serious problem in most genomic centers. To alleviate it, general purpose tools, such as gzip, are used to compress the data. However, although pervasive and easy to use, these tools fall short when the intention is to reduce as much as possible the data, for example, for medium- and long-term storage. A number of algorithms have been proposed for the compression of genomics data, but unfortunately only a few of them have been made available as usable and reliable compression tools.
resultsIn this article, we describe one such tool, MFCompress, specially designed for the compression of FASTA and multi-FASTA files. In comparison to gzip and applied to multi-FASTA files, MFCompress can provide additional average compression gains of almost 50%, i.e. it potentially doubles the available storage, although at the cost of some more computation time. On highly redundant datasets, and in comparison with gzip, 8-fold size reductions have been obtained. AVAILABILITY: Both source code and binaries for several operating systems are freely available for non-commercial use at http://bioinformatics.ua.pt/software/mfcompress/.
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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.