DNA

IBM's Bioinformatics Pattern Discovery Tools are applications ranging from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences and the interactive annotation of amino acid sequences. Additionally, annotations for more than 70 archaeal, bacterial, eukaryotic and viral genomes are available on-line and can be searched interactively.

Bioinformatic Harvester” caches and cross-links public bioinformatic databases and prediction servers to provide fast access to protein specific bioinformatic information. A ranking search engine retrieves most relevant information based on your query.

FAN server is for fingerprint analysis of nucleotide sequences.

DNannotator is tool for batch and custom annotation of regional genomic sequences.

The Virtual Ribosome is a comprehensive tool for translating DNA sequences to the corresponding peptide sequences.

Promoter2.0 predicts transcription start sites of vertebrate PolII promoters in DNA sequences. It has been developed as an evolution of simulated transcription factors that interact with sequences in promoter regions.

This program is designed for the prediction of cis-regulatory elements, for which short motifs (protein binding sites on the DNA) are known. Using these motifs, it is possible to search them on sequences, to weight them by applying a positive or negative training set (model or background, respectively) and to score a sequence.

Analysis and Annotation Tool for Finding Genes in Genomic Sequences.

Visualisation and analysis of transcription factor binding sites in nucleotide sequences.

NUMODs (nuclease-associated modular DNA-binding domains) can be found, in addition to a service that locates NUMODs on a given protein/DNA sequence.