Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Generates graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots. CGView can supply the sequences in different format (raw, FASTA, GenBank or EMBL). BLAST is used by the server to compare the sequence sets. Then, the results are converted in a graphical map which shows all the sequence. The web tool includes different options to control which types of features are displayed and how the features are drawn. The server can be used to aid in the identification of conserved or diverged genome segments, instances of horizontal gene transfer, and differences in gene copy number.
A suite of software tools that enable users to create high-quality visual representations of both circular and linear annotated genome sequences provided as GenBank files or accession numbers. Although all types of DNA sequences are accepted as input, the software has been specifically optimized to properly depict features of organellar genomes. The core processing components can be downloaded as a Perl module, thus also allowing for convenient integration into custom processing pipelines.
An interactive Java application for generating circular and linear representations of genomes. Making use of the Artemis libraries to provide a user-friendly method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational databases, it filters features of interest to display on separate user-definable tracks. It can be used to produce publication quality images for papers or web pages.
Constructs editable, publication-quality, maps of mitochondrial and chloroplast genomes and of large plasmids. GenomeVx indicates the location of genes and chromosomal features as well as a position scale on these maps. The program takes as input either raw feature positions or GenBank records. In the latter case, features are automatically extracted and colored, an example of which is given. Output is in the Adobe Portable Document Format (PDF) and can be edited by programs such as Adobe Illustrator.
A user-friendly web-based tool to create custom circular maps to aid the analysis of microbial genomes and sequence elements. Sequence related data such as gene-name, COG class, PFAM domain, GC%, and subcellular location can be comprehensively viewed. Quantitative gene-related data (e.g. expression ratios or read counts) as well as predicted sequence elements (e.g. regulatory sequences) can be uploaded and visualized. CiVi accommodates the analysis of genomic elements by allowing a visual interpretation in the context of: i) their genome-wide distribution, ii) provided experimental data and iii) the local orientation and location with respect to neighboring genes.
Serves to visualise genomic data of prokaryotic chromosomes. The GeneWiz browser allows users to perform various analyses like mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. This tool can produce a graphic on which user can study single nucleotides from different scale.