gff2aplot: Plotting sequence comparisons.

Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra -Centre de Regulació Genòmica, Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.
Bioinformatics (Impact Factor: 5.32). 01/2004; 19(18):2477-9. DOI: 10.1093/bioinformatics/btg334
Source: PubMed

ABSTRACT gff2aplot is a program to visualize the alignment of two sequences together with their annotations. Input for the program consists of single or multiple files in GFF-format which specify the alignment coordinates and annotation features of both sequences. Output is in PostScript format of any size. The features to be displayed are highly customizable to meet user specific needs. The program serves to generate print-quality images for comparative genome sequence analysis.
gff2aplot is freely available under the GNU software licence and can be downloaded from the address specified below.

1 Bookmark
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Embryonic development in nonmammalian vertebrates depends entirely on nutritional reserves that are predominantly derived from vitellogenin proteins and stored in egg yolk. Mammals have evolved new resources, such as lactation and placentation, to nourish their developing and early offspring. However, the evolutionary timing and molecular events associated with this major phenotypic transition are not known. By means of sensitive comparative genomics analyses and evolutionary simulations, we here show that the three ancestral vitellogenin-encoding genes were progressively lost during mammalian evolution (until around 30-70 million years ago, Mya) in all but the egg-laying monotremes, which have retained a functional vitellogenin gene. Our analyses also provide evidence that the major milk resource genes, caseins, which have similar functional properties as vitellogenins, appeared in the common mammalian ancestor approximately 200-310 Mya. Together, our data are compatible with the hypothesis that the emergence of lactation in the common mammalian ancestor and the development of placentation in eutherian and marsupial mammals allowed for the gradual loss of yolk-dependent nourishment during mammalian evolution.
    PLoS Biology 04/2008; 6(3):e63. · 12.69 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The authors propose a simple version of the dot-plot scheme to be used in the case when the distances between sequence elements may take more than two values. The method is applicable, in particular, to the case of the sequences of large-length windows when the sets of distance values are continuous. The proposed technique is simple to implement and the results can produce readable maps for further analysis. To illustrate its potentialities, the method has been applied to the comparison of genomic sequences. The asymmetry in the number of direct and reverse tracks for the Homo sapience genome has been discovered.
    Information Sciences 01/2011; · 3.64 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Comparative approach is one of the most essential methods for extracting functional and evolutionary information from genomic sequences. So far, a number of sequence comparison tools have been developed, and most are either for on-site use, requiring program installation but providing a wide variety of analyses, or for the online search of user's sequences against given databases on a server. We newly devised an Asynchronous JavaScript and XML (Ajax)-based system for comparative genomic analyses, CGAS, with highly interactive interface within a browser, requiring no software installation. The current version, CGAS version 1, provides functionality for viewing similarity relationships between user's sequences, including a multiple dot plot between sequences with their annotation information. The scrollbar-less 'draggable' interface of CGAS is implemented with Google Maps API version 2. The annotation information associated with the genomic sequences compared is synchronously displayed with the comparison view. The multiple-comparison viewer is one of the unique functionalities of this system to allow the users to compare the differences between different pairs of sequences. In this viewer, the system tells orthologous correspondences between the sequences compared interactively. This web-based tool is platform-independent and will provide biologists having no computational skills with opportunities to analyze their own data without software installation and customization of the computer system. Availability and Implementation: CGAS is available at
    Bioinformatics 03/2009; 25(7):958-9. · 5.47 Impact Factor

Full-text (2 Sources)

Available from
Jun 6, 2014