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    News & Commentary - Message forums
    lication examples available
    Submitted by Audrius Me?kauskas; posted on Thursday, November 13, 2003

    Submitter
    Despite the previous Sight versions were able to generate cross-platform java applications, they were later only modifyable by a programmer. Since 2.1.2 SP 1 it is possible to save the assembled web agent workflows in a team files (.tjar), alowing later modifications and subsequent code generation. This simple improvement allows us to suggest various examples of the application workflows, leading to easier understanding that can be done with this program.

    This release includes sample applications (web robot teams). You need at least version 2.1.2 service pack 1 to open them.

    Genome_walker.tjar performs analysis of the given DNA fragment or fragments, representing genome fragment or small (bacterial or viral) genome.

    Protein_explorer.tjar performs various analysis on the protein sequence, corresponding the given NCBI accession number. Can take some RNA sequences if the corresponding XML entry contains protein translation.

    Specific_range.tjar scans the 200 amino acids upstream the third transmembrane helix for PROSITE hits and NCBI conservative domains. The imput is the list of NCBI accession numbers to the protein sequences. As this is a public example, we used the simple and fast-responding servers.

    Blast_blast_blast.tjar can re-submit the received BLAST hits to BLAST similarity search again. The iteration is repeated 3 times. The team investigates problems and possibilites for this way of finding the similarity between proteins, also can be useful in understanding BLAST limitations.

    In future, we plan to release more examples. We would be glad to accept and display the user-created applications.
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