Computational protocol: Retrotransposon vectors for gene delivery in plants

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Protocol publication

[…] Sequences flanking mini-Tnt1 s were used as queries in BLASTN, BLASTX or TBLASTX searches against the non-redundant (nr) and EST databases at the National Center for Biotechnology information (NCBI, http://www.ncbi.nlm.nih.gov) or against the tobacco gene index (NtGI, http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=tobacco). Flanking sequences that returned high scoring pairs with e-values < 1.00E-5 were considered as significant. […]

Pipeline specifications

Software tools BLASTN, BLASTX, TBLASTX
Application Nucleotide sequence alignment
Organisms Saccharomyces cerevisiae, Nicotiana tabacum, Cauliflower mosaic virus
Chemicals Neomycin