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.

 

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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:

 

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