AMEN (Annotation, Mapping, Expression and Network) is a stand-alone, unified suite of tools to manage, explore and combine biological multifaceted high-throughput data such as annotation, chromosomal location, expression and interaction data.
BMT is combination of seven tools including FastqTrimmer, Gene Prediction, DNA Analysis, Translation, Protein analysis and Pairwise and Multiple alignment.
STINGRAY: system for integrated genomic resources and analysis.
Wagner G, Jardim R, Tschoeke DA, Loureiro DR, Oca?a KA, Ribeiro AC, Emmel VE, Probst CM, Pitaluga AN, Grisard EC, Cavalcanti MC, Campos ML, Mattoso M, Dávila AM.
BMC Res Notes. 2014 Mar 7;7:132. doi: 10.1186/1756-0500-7-132.
StrBio library is a set of Java classes useful for development of software for computational structural biology research. The StrBio library includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.
Catherine Belleannée, Olivier Sallou, Jacques Nicolas. Expressive Pattern Matching with Logol.
Application to the Modelling of -1 Ribosomal Frameshift events. JOBIM 2012- 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2012, Rennes, France. pp. 5-14.
TREVA (Targeted REsequencing Virtual Appliance) is a user-friendly virtual appliance, containing complex bioinformatics pipelines that can be installed and setup with minimal efforts. TREVA pipelines support a series of analyses commonly required for targeted resequencing and whole exome sequencing data, including: single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses.
ORCA is a platform for bioinformatics analysis. It is suited for those wishing to conduct self-serve analysis using their own existing data. Hundreds of bioinformatics tools from Brewsci/bio are installed in the ORCA Docker image using Linuxbrew.
TAGOPSIN (TAxonomy, Gene, Ontology, Protein, Structure INtegrated) retrieves select data from NCBI Taxonomy, NCBI Nucleotide, UniProtKB, Gene Ontology, Pfam, EBI SIFTS and RCSB PDB, and assembles them in the database management system PostgreSQL. TAGOPSIN is an organism-centred data warehousing tool that works with prokaryotic and eukaryotic organisms as well as viruses.
