Table 3 Sequence similarity program-query-database combinations used to search for TE-related host sequences
From: Evaluating the protein coding potential of exonized transposable element sequences
Tool | Query | Database |
|---|---|---|
HMMER | PDB/Swiss-Prot protein | HMM profiles of TE-related Pfam domains |
BLASTN | TE CDS & all TE sequences | PDB/Swiss-Prot CDS |
BLASTP | TE protein | PDB/Swiss-Prot protein |
BLASTX | TE CDS & all TE sequence | PDB/Swiss-Prot protein |
TBLASTN | TE protein | PDB/Swiss-Prot CDS |
TBLASTX | TE CDS & all TE sequence | PDB/Swiss-Prot CDS |
RepeatMasker | PDB/Swiss-Prot CDS | TE CDS & all TE sequences |