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SSHdb

SSHdb is a tool for sequence management and annotation of SSH cDNA libraries. SSHdb manages different SSH libraries as different projects. A user can register for specific projects in order to view the top table and sequence information linked to that project.

  1. Input to SSHdb:

    • Top tables (gene-lists ranked in terms of differential expression) after a SSHscreen or limma (linear models for microarray data) analysis.
    • Sequences of individual cDNA fragments in FASTA format.
  2. When FASTA sequences are uploaded:

    • Vector sequences are removed.
    • Redundant partners in the library are identified.
    • Each sequence is annotated with putative BlastX/BlastN functions.
  3. The user can:

    • View and select the preferred annotation from the top 10 BLastX and BlastN hits.
    • Download the alignment of each redundant partner group.
    • Change the representative clone of each redundant partner group.
    • Re-Blast sequences.
    • Export annotated FASTA sequences and top tables.

 

To view the Cowpea demo data, use the following login:

  • Username: guest
  • Password: sshcp
  • Note: This user is able to view/download data, but not upload/edit data.

    Reference:

    Coetzer N, Gazendam I, Oelofse D, Berger DK (2010) SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpea. Plant Methods 6: 10. Open Access: http://www.plantmethods.com/content/6/1/10.