About Search by Sequence
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Search by Sequence performs a nucleotide-nucleotide or protein-translated nucleotide BLAST search against
Addgeneâs plasmid sequence database.
BLAST returns plasmids with similarity to the query sequence.
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Results are sorted by E-value, a statistic from BLAST that describes the significance of a match.
Lower values are considered better matches.
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FASTA headers and numbers at the beginning of each line will be removed.
The query should only contain DNA characters.
Tips for Success
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Enter a distinct sequence that is an important, differentiating feature. For example, the coding region of
a gene, instead of the plasmid origin of replication.
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Inspect the percent identity, query coverage, and alignment details to determine if a result match is satisfactory.
Visit the corresponding plasmid webpage to view additional details about a matching plasmid.
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If no results are returned:
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Try a different isoform or region of the desired sequence.
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Choose a different BLAST database. Try the general âAll Addgene Plasmidsâ (default selection),
instead of a specific database, such as âPlant Expression Plasmidsâ
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Try selecting a different BLAST algorithm:
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megablast: Designed for comparing sequences within the same, or closely related, species.
Default selection.
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blastn: Designed for comparing sequences from different species. May return additional results,
if exact species match is not required.
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blastn-short: Optimized for searching with shorter sequences (<= 30 nucleotides)
but can still be effective with slightly larger sequences.
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tblastn: Designed for comparing protein sequences against a translated nucleotide sequence database.
Helpful for finding plasmids with codon-optimized sequences.
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tblastn-fast: A faster version of tblastn that may return results more quickly, but is less sensitive
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There may not be a match in our database.
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You can adjust the Max Results setting on the results page from 25 to 500. If many sequences share the same top E-value,
only a truncated set of equally high-scoring matches will be shown. Set the Max Results to 500 to see more matches.
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Fill out our Suggest a Plasmid form or
e-mail [email protected] to let us know what we're missing.
By using search by sequence, you understand that some sequences are subject to our Terms of Access and the restrictions contained therein.
