About
GTO is a toolkit for genomics and proteomics, namely for FASTQ, FASTA and SEQ formats, with many complementary tools. The toolkit is for Unix-based systems, built for ultra-fast computations. GTO supports pipes for easy integration with the sub-programs belonging to GTO as well as external tools. GTO works as LEGOs, since it allows the […]

A survey on data compression methods for biological sequences.
Domains: protein sequences, genomic sequences (reference-free and reference-based) and specific formats (FASTA, FASTQ, SAM/BAM).

Compress and analyze genomic sequences. As a compression tool, GeCo is able to provide additional compression gains over several top specific tools, while as an analysis tool, GeCo is able to determine absolute measures, namely for many distance computations, and local measures, such as the information content contained in each element, providing a way to quantify and locate specific genomic events. GeCo can afford individual compression and referential compression.

Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For visualisation, Smash outputs a SVG image, with an ideogram output architecture, where the patterns are represented with several HSV values. It can perform both in small- and large-scale.

EAGLE is an alignment-free method and associated program to compute relative absent words (RAW) in genomic sequences using a reference sequence. Currently, EAGLE runs on a command line linux environment, building an image with patterns reporting the absent words regions (in SVG) as well as reporting the associated positions into a file. EAGLE hast got scripts to run on the current outbreak 99 ebola virus genomes (using the human as a reference), including the download, filtering and processing of the entire data.

MENT is a set of tools for lossless compression of microarray images. These tools can also be used for other types of images such as medical, RNAi, etc. This set of tools are divided into two categories. One where a bitplane decomposition approach is used and the other one where a binary tree decomposition is used.

XS is a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity. It has several running modes, depending on the time and memory available, and is aimed at testing computing infrastructures, namely cloud computing of large-scale projects, and testing FASTQ compression algorithms. Moreover, XS offers the possibility of simulating the three main FASTQ components individually (headers, DNA sequences and quality-scores)

SACO is a method to handle the DNA bases and gap symbols that can be found in MAF files. SACO is based on a mixture of finite-context models. Contrarily Hanus et al approach, it addresses both the DNA bases and gap symbols at once, better exploring the existing correlations. For comparison with previous methods, our algorithm was tested in the multiz28way dataset. On average, it attained 0.94 bits per symbol, approximately 7% better than the previous best, for a similar computational complexity.

MAFCO is a lossless compression tool specifically designed to compress MAF (Multiple Alignment Format) files. Compared to gzip, the proposed tool attains a compression gain from ≈ 34% to ≈ 57%, depending on the data set. When compared to a recent dedicated method, which is not compatible with some data sets, the compression gain of MAFCO is about 9%.

Machine learning system to classify metagenomic samples.

DNAatGlance is a program for the detection of large-scale genomic regularities by visual inspection. Several discovery strategies are possible, including the standalone analysis of single sequences, the comparative analysis of sequences from individuals from the same species, and the comparative analysis of sequences from different organisms.

MFCompress is a compression tool for 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 data sets, and in comparison with gzip, 8-fold size reductions have been obtained.

Variobox is a desktop tool for the annotation, analysis and comparison of human genes. Variant annotation data are obtained from WAVe, protein metadata annotations are gathered from PDB and UniProt, and sequence metadata is obtained from Locus Reference Genomic (LRG) and RefSeq databases. By using an advanced sequence visualization interface, Variobox provides an agile navigation through the various genetic regions.

NCCD is a method and package tool designed to compute the Normalized Conditional Compression Distance.

The mRNA optimiser is a tool that redesigns a gene messenger RNA to optimise its secondary structure, without affecting the polypeptide sequence. The tool can either maximize or minimize the molecule minimum free energy (MFE), thus resulting in decreased or increased secondary structure strength.

EuGene is a gene redesign software. It allows opening and parsing genome files, loading genes into a workspace, and redesign the genes according to many redesign methodologies such as enhancing codon usage, codon context, GC content, hidden stop codons, repeated codons or nucleotides, harmonizing genes to other host species, avoiding deleterious sequences, among others. EuGene is free and auto-updates so you can always be up to the latest features and corrections.

GReEn (Genome Resequencing Encoding) is a tool for compressing genome resequencing data using a reference genome sequence. It overcomes some drawbacks of the recently proposed tool GRS, namely, the possibility of compressing sequences that cannot be handled by GRS, faster running times and compression gains of over 100-fold for some sequences.

The Genomic Name Server is an innovative data integration system that incorporates a large set of heterogeneous biological data under a simple yet powerful schema. GeNS also addresses the cross-database low identifier coverage issue by proposing a new methodology of data integration.

MIND is a repository of microarray experiments that handles storage, management and analysis of microarray data. It is supported by an infrastructure prepared to integrate dynamically further functionalities (Quality Control assurance, data processing, data mining, visualization, reports, etc.).

ANACONDA is a software package specially developed for the study of genes’ primary structure. It uses gene sequences downloaded from public databases, as FASTA and GenBank, and it applies a set of statistical and visualization methods in different ways, to reveal information about codon context, codon usage, nucleotide repeats within open reading frames (ORFeome) and others.