Comparative genome visualization software tools | DNA annotation
Comparative genomics aims at comparing the structure and function of genomes from different species. At the crossroad between evolutionary sciences and genomics, its major application is the discovery of new genes or gene functions.
A free tool for displaying pairwise comparisons between two or more DNA sequences. ACT can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation.
Displays large volumes of genomic rearrangement data. Circos is a visualization tool that applies a circular ideogram layout to display relationships between genomic intervals. The software provides a scalable means to illustrate relationships between genomic positions and is designed to allow flexible and easy rearrangement of elements in the image. It also contains several tools to help analyze, filter, and format data.
A Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures.
Allows users to confront two long genomic sequences and to recognize conserved segments between them. PipMaker supports analysis of unfinished or “working draft” sequences by permitting the second sequence to be in unoriented and unordered contigs. It can make comparison of genomic sequences from any two related species. This tool uses the alignments to map each position in the exons file for the first sequence onto the corresponding position in the second sequence.
Enables identification of identical and proximate markers between linkage maps. MapComp permits users to compare genetic maps built from related species with or without the same RADseq protocol. It uses a reference genome of a related species as an intermediate This software is able to supply a detailed characterization of the homologous and homeologous chromosome arms representing all major genera included in the salmonid family.
Allows to compare genomic sequences. WebACT is an online resource providing BLAST comparison and sequence files in appropriate formats for ACT. It permits the generation of comparisons based on sequences contained within the EMBL database or selected from a database of pre-computed comparisons. The comparisons which are done on the web tool can be viewed online through a version of ACT that uses Java Web Start.