The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species

Abstract

The Iccare web server, http://genopole.toulouse.inra.fr/bioinfo/Iccare, provides a simple yet efficient tool for crude EST (expressed sequence tag) annotation specifically dedicated to comparative mapping approaches. Iccare uses all the EST and mRNA sequences from public databases for an organism of interest (query species) and compares them to all the transcripts of one reference organism (Homo sapiens or Arabidopsis thaliana). The results are displayed according to the location of the genes on the chromosomes of the reference organism. Gene structure information and sequence similarities are combined in a graphical representation in order to pinpoint the nature of the transcript query sequence. The user can subsequently design primers or probes for the purpose of physical or genetic mapping. In addition to the query organisms already available in Iccare, users can perform a tailor-made search with their own sequences against the animal or plant reference organism genes.

Figure 1

Global chromosome synteny. Example of human chromosome 22 gene map for the query species Bos taurus at the chromosome scale on the left and at a higher resolution on the right. From left to right, the human chromosome image displays map locations in Mb and a cytogenetic map with alternating dark and light bands, with a dark-and-white check pattern for the centromeric region. The dark-yellow arrowed rectangles display the conserved syntenic segments shared with the mouse genome. To the right, the corresponding conserved syntenic segments of the mouse genome are displayed in colors corresponding to the mouse chromosome. The buttons on the left enable the user to move to different regions at different levels of resolution. The genes colored in green correspond to human genes for which sequence similarities have been observed to bovine sequences. Human genes without significant similarities to bovine sequences are shown in blue. The mouseover on a gene provides a link that gives access to detailed information about the alignments (see Figure 2).

Figure 2

Gene structure representation and local alignment. (A) The Arabidopsis gene structure of At4g03280 and Helianthus annuus sequences with homologous regions with this gene are shown. The top graphical box contains gene structure information related to the A.thaliana gene—intron/exon structure of genomic DNA. The green boxes represent the exons, which are concatenated on the second line, mimicking the transcription process. The numbers on top of the first line correspond to intron size. The third line recalls the transcript sequence with a particular emphasis on the translated region, shown in dark blue. The bottom graphical box contains H.annuus sequences and representation of local similarities to the Arabidopsis gene At4g03280; information for each query sequence is located to the left (GenBank ID, sequence size and BLASTN E-value) and the sequence representation is on the right: the black line symbolizes the sequence. Green boxes correspond to sequence similarities with the Arabidopsis gene on the same strand, while yellow boxes correspond to similarities in a reverse-complement manner. Sequence similarities to additional query species are also available (‘plus’ buttons). (B) The display associated with the result of a local alignment between Arabidopsis gene At4g03280 and the H.annuus EST sequence CD847222. BLASTN information (score, E-value, identities, gaps and strand) is placed on the top. The query nucleic sequence is represented in black and the Arabidopsis nucleic sequence is represented in alternate blue and mauve letters corresponding to the different exons.