Welcome to SIMAP.
SIMAP is a database containing the similarity space formed by about all amino-acid sequences from public databases and completely sequenced genomes.
You may find sequences and protein entries of interest by fulltext search which uses an index of proteins IDs, accession numbers and descriptions, and the Biothesaurus.
Starting from your query sequence you may find the nearest sequences in SIMAP. By searching parts of your query in a suffix array of all SIMAP sequences (generated by VMATCH), this search runs much faster than BLAST.
- 2013, Dec 14: Next release scheduled for Feb 2014
The next release of SIMAP is scheduled for February 2014. The delay is caused by the approx. 6 million new sequences imported from the restructured NCBI RefSeq database in Aug 2013. Due to the limitation of our computational capacity to about 1.2 million sequences per month, the calculation of hits for these sequences is still ongoing. The new release will also be upgraded to the latest Interpro release.
- 2013, Dec 14: Removal of metagenomes and re-calculation of SIMAP
We going to migrate the entire SIMAP database in 2014 to a new algorithm for sequence similarity calculation. We will not longer use FASTA heuristics but switch to the exact Smith-Waterman algorithm. The scoring by BLOSUM50 will be continued, but will incorporate composition-based score adjustment, such as in BLAST. During the migration we will maintain the current, FASTA based SIMAP, thus keeping SIMAP up-to-date and online. However, in order to minimize the computational and storage requirements, we will temporary remove those metagenomes from SIMAP that were imported from IMG/M, Camera, HMP and ENA/WGS. Only environmental sequences in ENA (from Uniprot/TrEMBL) will remain. Metagenomes will be integrated again after the migration of the non-metagenomic SIMAP to the new algorithm has been finished.
If you urgently need sequences of particular metagenomes, please inform firstname.lastname@example.org as soon as possible. We will then check if we can keep these in SIMAP.
- 2013, Sep 15: New Web Service and DAS online
The new Axis 2 Web Service and the new Distributed Annotation System (DAS) service are online (see Web Services page for URLs and further instructions)
- 2013, Sep 15: New submatrix export tool online
A new version of the submatrix export tools has significantly improved the performance and provides a lot more options for users who need parts of the SIMAP sequence similarity matrix
- 2013, Jun 21: InterPro 43.0 integrated
InterPro annotations have been upgraded to version 43.0 in the June 2013 release of SIMAP.