Bioinformatics/DNA Search
Posted: Sun Nov 13, 2011 9:34 pm
Note that this functionality is still very much Under Construction and I am looking for user feedback to drive development.
V13 introduces a Bioinformatics/DNA search option which lets you search for amino acid strings and IUPAC codes in files containing DNA sequences.
When doing a search, two new options are available - Amino Acid Search and IUPAC Search. When one of these options is selected, the search string is treated as either a string of amino acid codes orIUPAC nucleotide codes.
Only exact matches are found. Imperfect matches (as in BLAST searches) are not supported.
Note that by default, these new options are hidden from the user. To enable the new functionality, you must enable the BioInformatics/DNA search option in the Search section of Preferences.
Amino Acid Search
When the Amino Acid Search option is selected, the search string is treated as a sequence of amino acid codes.
There are 20 valid codes which represent the 20 standard amino acids (ACDEFGHIKLMNPQRSTVWY). An X is used to indicate any amino acid and a * is used to indicate a stop codon.
V will search the file (containing DNA sequences) and will match any sequence that corresponds to the entered amino acid string.
The screenshot below shows the result of searching for an amino acid string of GRGDS
IUPAC Search
When the IUPAC Search option is selected, the search string is treated as a sequence of IUPAC nucleotide codes.
There are 15 valid codes which correspond to the valid characters in the DNA/RNA alphabet (ACGTURYMKSYNDHV), and N is used to indicate any nucleotide.
The screenshot below shows the result of searching for an IUPAC nucletode string of TATAWAAM
V13 introduces a Bioinformatics/DNA search option which lets you search for amino acid strings and IUPAC codes in files containing DNA sequences.
When doing a search, two new options are available - Amino Acid Search and IUPAC Search. When one of these options is selected, the search string is treated as either a string of amino acid codes orIUPAC nucleotide codes.
Only exact matches are found. Imperfect matches (as in BLAST searches) are not supported.
Note that by default, these new options are hidden from the user. To enable the new functionality, you must enable the BioInformatics/DNA search option in the Search section of Preferences.
Amino Acid Search
When the Amino Acid Search option is selected, the search string is treated as a sequence of amino acid codes.
There are 20 valid codes which represent the 20 standard amino acids (ACDEFGHIKLMNPQRSTVWY). An X is used to indicate any amino acid and a * is used to indicate a stop codon.
V will search the file (containing DNA sequences) and will match any sequence that corresponds to the entered amino acid string.
The screenshot below shows the result of searching for an amino acid string of GRGDS
IUPAC Search
When the IUPAC Search option is selected, the search string is treated as a sequence of IUPAC nucleotide codes.
There are 15 valid codes which correspond to the valid characters in the DNA/RNA alphabet (ACGTURYMKSYNDHV), and N is used to indicate any nucleotide.
The screenshot below shows the result of searching for an IUPAC nucletode string of TATAWAAM