Tips for Using BLAST to Verify Plasmids
Type
Blog Post
Published
May 29, 2014, 1:29 p.m.
... from the dropdown menu. Typically, we use the default nucleotide database “Nucleotide collection (nr/... as well as the overall alignment results. The default setting is “Optimize for Highly similar sequences...results.
When using blastx at Addgene, we use the default “Non-redundant protein sequences (nr)” database...repeated or highly homologous regions, which by default are ignored in a standard blastx search. An alignment...have found it saves analysis time to remove this default setting.
Timesaving Tip #2: blastx searches are...searches do not filter low complexity regions by default, meaning that you do not have to remember to adjust...adjust any blastp algorithm parameters. We use the default scoring matrix BLOSUM62, but you may want to check...