Oligonucleotide design
The design of long oligos can be performed for any number of DNA sequences. The DNA sequence should be provided in a FASTA or txt format. You can also provide a list of the accession numbers of your favorite genes.
For oligonucleotide probes design, we use dedicated algorithm, which applies a variety of simple filters to select the most specific region of a given gene by skipping regions with contiguous bases common in other sequences. Sequences with at least 96% identity to the query sequence and with an alignment equal to or greater than the query length are considered redundant and removed.
Because cross-hybridization will occur between regions with contiguous or perfectly matched bases, the primary filter rejects potential probes that contain ≥ 15 perfect base-matches with any other input sequence. Sequence regions similar to non-coding RNAs are also discarded because total RNA is often used for array hybridization.
Low-complexity regions are filtered out to maintain oligo specificity. Oligos and sequence regions that may form secondary structures are discarded since both the probes and the sequence target sites should be easily accessible for hybridization
Finally, oligo specificity is double-checked using local Blast search against a reference database containing the complete genome sequence.
The oligo program will generate a score for the uniqueness of all potential probes of the input sequences and select the best oligos according to the specified parameters such as palindrome structure, GC content and internal repeat. Oligo length is user fixed from 15 to 60 bases, and the target temperature ± delta is user defined. All oligos will have similar Tm, which will help you to use homogeneous hybridization and washing conditions.
| Name |
Quantity |
Reference |
EUR |
|
| Oligo design up to 70 bases |
1 |
AR-LOLIG-DE |
Upon request |
|