The database query subtask performed a batch similarity search of a database using SubSeq as the queries. The BLAST program used was the NCBI Blastall -p blastn version 2.12 with a defined set of parameters. The masking of low complex regions was performed for the seeding phase to speed up the query; however, low complexity repeats were included in the actual scoring. The entire nucleotide database from NCBI acquired on February 7, 2006 was used as the reference database. (Note that earlier images of the database were used during development but all experiments were rerun with the algorithm as described with the Figure 3 . Detailed schematic representation of the second subtask of ProSeq identification Task(I), organism identification for an individual SubSeq. Each SubSeq sent to BLAST returned a list of possible matches contained in a Return array that was sorted through to find best bit score/expect value pair (MaxScore). If the MaxScore was greater than MIN (10 À6 ), all returns that had this best Score were sorted into a new array Rank1. Detailed SubSeqs requirement is described in Supplementary Data.