Spectra remained unmatched by database searching were interpreted de novo using following sequencing parameters: fragment mass deviation, 0.002 Da, and ladder score (percentage of expected y- and b-ions) exceeding 40.
The WCR unigenes with no match to the nr database (unmatched) may represent novel genes with functions not yet been identified, or they could be a product of assembly errors.
In terms of the assignment at the phylum level, Firmicutes (52.79%) and Bacteroidetes (41.57%) were predominant in the gut bacteria of mice, followed by Tenericutes (3%), Actinobacteria (0.18%), Cyanobacteria (0.023%), and Proteobacteria (0.0042%), with 2.41% sequences unmatched with the database (see Supplemental Material, Figure S2B).
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However, additional FcB1-schizont-ESTs matching other MSP1 variants were discovered by comparing unmatched ESTs to the UniProt database using the BLAST algorithm.
An InterProScan search [ 46] of these unmatched WCR unigenes against the nr database revealed hits to the protein signature databases for 2,357 out of 5,762 (41%), suggesting that many have homologs in other species that were undetected using BLASTx alone.
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Of the unmatched contigs, 766 had matches in the Pfam database and 31 had matches in the Rfam database, indicating at least part of unmatched contigs represent real transcript.
After running the unmatched contigs against UTRdb [ 22], a database of 5' and 3' untranslated regions (UTRs) of eukaryotic mRNAs, we found another 3,658 contigs that were homologous to UTRs, indicating that these contigs might represent the UTRs of common carp protein-coding genes.
