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PROMPT-Fast-Mapping (PROMPT-FM)
PROMPT-Fast-Mapping allows you to map your input to really huge databases up to 50-times° faster than BLAST.
You can map any FASTA file with amino acid sequences or protein identifier lists immediately against all standard gigantic databases like UniProt or GenBank. No download or local installation of any of these databases is necessary (All required data is retrieved via web services).
Example: Here we show you the speed up of the mapping of a small sample of 500 proteins against some gigantic databases°
| Database | # Sequences in the DB | Time BLAST | Time PROMPT | PROMPT times faster |
| UniProtKB/TrEMBL rel. 8.2 | ~ 3 000
000 |
~6 hours |
~7 minutes |
>50
x |
| UniProt/Swiss-Prot rel. 8.2 | ~ 200 000 |
~70 minutes |
~7 minutes |
~
10 x |
Additionally you can map your proteins against one or more specific genomes that are included in our PEDANT database (currently >400 genomes) or other databases like PDB or NCBI-COGs.
°) Exhaustive evaluations and method details will be provided in our upcoming publication. The BLAST speed stated may vary depending on your CPU power (here we used a Intel Pentium 4 CPU with 2.66 GHz and 2 GB RAM)