Tools

Tools

Sma3s

Sma3s — Sequence massive annotator using 3 modules — is a bioinformatics tool for the automatic functional annotation of large-scale sequence datasets, including proteomes and transcriptomes. It assigns biological information such as putative function, cellular localization, biological process and protein structure using three complementary annotation modules based on exhaustive BLAST searches. Sma3s is designed to be accurate, easy to use and computationally lightweight, producing spreadsheet-friendly output files suitable for downstream analysis and visualization.

You can download it here.

ASACO

ASACO — Automatic and Serial Analysis of CO-expression — is a bioinformatics web application designed to explore gene co-expression patterns across large collections of public transcriptomics experiments. Given a query gene, ASACO identifies positively and negatively correlated genes, helping researchers uncover functional relationships, potential regulators, disease-associated genes, and candidates for drug repurposing.

  • AnABlast is a bioinformatics tool for discovering new and ancestral protein-coding genes in genomic sequences. It detects short evolutionary signals from low-score protein alignments, helping to reveal coding regions that conventional gene finders may miss, including novel genes, exons, pseudogene regions and small open reading frames.
  • orthoFind is a bioinformatics web application for the rapid discovery of homologous and orthologous proteins from one or more query sequences. It searches reference proteomes, Swiss-Prot or user datasets, and complements the results with functional annotation and protein domain architecture analysis.
  • AnaGram is a bioinformatics tool for the functional annotation of non-conserved or poorly characterized proteins. It identifies short significant sequence fragments, known as protomotifs, and links them to functional annotations from protein and literature databases, helping to infer possible functions when conventional homology-based methods are not informative.
  • semirna is a bioinformatics web tool for predicting and searching plant microRNAs. It uses putative target sequences, such as mRNAs, to identify candidate miRNAs in plant genomes, and can also help evaluate small RNA sequencing candidates and search for miRNAs in newly sequenced genomes using homology.