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The selected contig sequences were filtered by secondary structure analysis.
SCOP domain sequences were filtered at 90% identity.
Genomic sequence entries such as chromosome fragments or genome shotgun sequences were filtered out.
The SNP positions in the RefSeq sequences were filtered by the RefSeq gene coordinates.
Metagenomic sequences were filtered using a BlastX search against the Pfam database [43].
Low quality sequences, transposable element and putative contamination sequences were filtered (see Methods S1).
All unique sequences were filtered to remove sequence copies and only keep sequences with at least 300 bp.
For the HA segment, non-H1 sequences were subsequently filtered; similarly, non-N1 sequences were filtered from the NA collection.
Low complexity sequences were filtered with SEG [45], and 10−5 was chosen as the E value cut-off.
Lastly, sequences were "filtered" for possible contaminants such as the E. coli genome, vector DNA, mitochondrial DNA, ribosomal RNA, and viral DNA using BLASTN.
These sequences were filtered to remove entries where the only entry on the annotation line was 'unidentified bacterium' or 'uncultured bacterium', leaving 97987 entries.
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