- Name Change and Copyright
- The name of the system has been changed to OpenFreezer and Copyright Information has been added to the documentation page.
- Protein Sequences
- Introduced mechanisms to translate Insert DNA sequences into protein upon Insert creation and modification.
Details: The longest ORF for the DNA sequence is determined by translating in all 3 frames and selecting the longest sequence between stop codons. The open/closed property of inserts is taken into account such that if no ATG is present, the translation starts at the first nucleotide and continues until a stop codon is reached. Similarly, if no stop codon is present, the translation continues until the end of the sequence. Note that this program does not check the longest ORF against predicted Ensembl or NCBI peptides and in rare cases the longest ORF does not match to a predicted peptide from genomic sequences.
Therefore, to ensure correct sequence translation, the Type of Insert and Open/Closed fields have been made mandatory on Insert Creation page. Specifically, one cannot leave the Type of Insert empty, but Open/Closed can be left blank if the type of insert is cDNA with UTRs, DNA Fragment or None. Error messages are produced in case of incorrect input. Functional verification, such as "an 'ORF' insert cannot have its open/closed property set to 'Non-Coding'", has not been included in translation.
The translated protein sequences are shown on the Insert Detailed View, indicating CDS frame, length, start and end positions.
- DNA sequence validation on creation and modification views
- On exit from Reagent Creation or Modification view, if DNA sequence contains characters other than A, T, C, G, or N, a warning message is displayed, notifying the user of the error, and either giving him/her the option of changing the sequence manually, or proceed with saving the sequence, automatically filtering out all unwanted characters from it.
- Improved Search Interface
- Made search more user-friendly by allowing to limit the search to specific reagent categories/properties. Still, search by keyword remains the core principle. Planning to expand the search beyond simple properties, introduce search by association, search for comments/description, search by protein/nucleotide sequence and restrict the search to specific packet.
- Redesigned the insert summary view to show different properties.
- Length for both oligos and inserts in the summary view still need to be updated dynamically.
- Primer Designer
- Added ability to design primers for any protein sequence. Links to the primer design page are available from Insert Detailed View and Search page. There is currently no functionality to store the generated primers in the database - planned for next release.
Details: A user chooses the boundaries at the protein level for the insert they wish to make. That protein sequence and corresponding cDNA sequence is then displayed. A user is given the option to add linkers to the ends of the PCR primers based on an inputted sequence or selection from a drop-down list. The user is then asked to limit the primers first by size of primer (including linkers) and then by Tm (without linker). Primers are then generated adding one nucleotide at a time until either the Tm or size limit is reached. The primers are displayed for the user and information on Tm (+/- linker) and MW is given.
- Tm (>10 & <14 nt's) = 4 (#G + #C) + 2(#A + #T)
- Tm (>14) = 64.9 +41*(#G+#C-16.4)/(sequence length)
- MW = (#A x 313.21) + (#T x 304.2) + (#C x 289.18) + (#G x 329.21) - 61.96
Please note that the Tm calculation assumes standard conditions of 50 nM primer, 50 mM Na+, and pH 7.0. The subtraction of 61.96 gm/mole from the molecular weight takes into account the removal of HPO2 (63.98) and the addition of two hydrogens (2.02) at the 5' end.
Entering a length value to limit primer size is not mandatory; however, Tm must be filled in (a warning is issued otherwise). If a length restriction is not provided, primer generation terminates once the requested Tm is reached; if both length and Tm values are filled in, the length of the primer would not exceed the length provided by the user (please see explanation on the Primer Design view).
- Automatic Tm and MW computation for Oligos
- Tm and MW are calculated automatically during Oligo creation and/or modification.
- Location link from Reagent Detailed View
- Added a 'Location' link from Reagent Detailed View to the reagent's location. If there is no location to report once a location link is pressed, the wording has been changed and provides a link back to the detailed view.
- Location Select All/Deselect All
- An option to select or deselect all from a container detailed view has been added. This button allows a user to create or modify an entire plate without having to select each well individually.