Web-based tools

This page lists web-based tools and applications for computational biology developed by UF researchers.


High-throughput annotation of genomic data

Genephony is a web-based tool to manage large datasets of biological information. Genephony allows you to easily create sets of biological objects from queries, uploading files, or deriving them from other existing sets. Sets can be browsed, sorted, filtered and merged; the resulting annotated datasets can be exported in a variety of common formats. Other features of Genephony include interoperability with the UCSC Genome Browser and Galaxy, and a SOAP interface to integrate it in a computational annotation pipeline.


Alternative splicing isoform signatures

Isoform Signatures are short, simple identifiers that univocally describe the structure of an alternative splicing isoform. Isoform signatures only depend on the exact intron-exon structure of a transcript, while they are independent of its location on the genome and of its sequence, and are designed to be easily included in publications and in databases. The Genesig server allows you to generate isoform signatures given a gene structure, or to look them up in a database of pre-computed signatures of known and predicted transcripts.


Computational detection of Transcription Factor Binding Sites

MAPPER is an integrated platform for the computational analysis of Transcription Factor Binding Sites (TFBS) in multiple genomes. It includes a library of over 1,000 TFBS models, a database of predicted binding sites in the promoters of all human, mouse and Drosophila genes, a search engine to scan user-provided sequences in real time, and rSNPs-MAPPER, a tool to predict the effect of Single Nucleotide Polymorphysms on TFBSs. Other MAPPER features include: a tool to create new TFBS models from binding site alignments, extensive data annotation and export capabilities, and a powerful, user-friendly interface.


The Tree Of Life Knowledge and Information Network

TOLKIN is an information management and analytical web application to provide informatics support for phylodiversity and biodiversity research projects. As a web-based application, TOLKIN is able to support collaborative projects by providing shared access to a variety of data on voucher specimens, taxonomy, bibliography, morphology, DNA samples and sequences.