Bioinformatics and Genomics Node

  Promoter analysis

ESTs assembly

Gene predictions

All the following Workflows have been implemented using taverna software. You can download the workflows and load them in your local taverna installation.
  • GeneID workflows:

    The following workflow takes a genomic sequence in FASTA format, runs geneid, then translates the gene predictions into a set of peptide sequences in order to run various software (blastp, pfam search etc.) that take peptide sequence input, giving some hints about the function of the predicted genes.

    Taverna Input document example:

  • SGP2 workflows:

    SGP2 software is an adaptation of geneid that takes into account synteny data, in order to improve the accurracy of the predictions.
    The synteny data are computed using a syntenic sequence from another organism and by performing tblastx search. The following workflow takes two syntenic sequences in FASTA format, runs tblastx, then runs SGP2 on the sequence you wish to perform the gene predictions, and finally translates the gene predictions into a set of peptide sequences.

    Taverna Input document example:

  • Workflows running both geneid and SGP2:

    The following workflow runs both geneid and SGP2 and generates an annotation map using gff2ps to visualize the annotations in order to compare them.

    Taverna Input document example:
    The following workflow is very similar to the previous one. In addition, it also takes a reference set of gene annotations in GFF format that can be compared to the predictions from geneid and SGP2.

    Taverna Input document example: