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"Plant DNA bar-coding efforts will need a similar investment before the reference database will be of comparable depth".
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As illustrated in Figure 3, before database searching, both the reference database and the query are clustered at certain similarity thresholds.
Before mapping the reads to the reference database, we filtered all sequences to remove adaptor sequences, low quality sequences, empty tags (sequences with only adaptor sequences), and tags with a copy number of 1 (probably resulting from sequencing errors).
Quek, X. C. et al. lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs.
We first screened the reference database for individuals from closely related speices based on p-distance between the unknow query and sequences in the database.
The reference database was represented by 286 family reference profiles with diverse pedigrees.
Phase identification was carried out using the reference database software.
Suspicious reference sequences were compared by BLAST against NCBI non-redundant nucleotide database and removed from the reference database.
The reference database contained 44,382 unigenes.
*Similarity in comparison with the reference database.
The reference database was dereplicated using the USEARCH algorithm [ 20].
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