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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.
Input to SSHdb:
- Top tables (gene-lists ranked in terms of differential expression) after a
or limma (
linear models for microarray data) analysis.
- Sequences of individual cDNA fragments in FASTA format.
- Top tables (gene-lists ranked in terms of differential expression) after a SSHscreen or limma (
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.
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:
Note: This user is able to view/download data, but not upload/edit data.
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.