Help:Sequencing Tool:Automatic Assessment Algorithm

The Registry provides a tool to automatically align and evaluate sequences against the sequence of a specified part. This is how that algorithm works as of 18 March 2008.

Definitions

Target Part - This algorithm only evaluates sequence reads against the sequence for a known part. It is not used to align sequence reads and then search for matching parts in teh Registry.

Sequence - A string of bases A, C, G, and T indicating nucleic acids, or N, indicating one unknown base.

Quality - A string of numbers corresponding one-to-one with bases in a sequence.

Sequence Read - The called set of bases from a sequencing reaction.

Raw Sequence - A sequence read as received from the sequencing center.

Forward Sequence - A sequence read on the same strand of DNA and in the same direction as the sequence of the target part. Forward sequences are a result of a forward primer. Forward sequences have been read frm left to right.

Reverse Sequence - The reverse compliment of a sequence read that extended from right-to-left along a target part. The sequencing program converts all raw sequences to either forward or reverse sequences based on the primer used.

New Sequences

When a new sequence is entered or new quality information is entered for a sequence, the software searches for the BioBrick™ prefix and suffix using this algorithm:

The BioBrick Prefix

Best Matching Sequences

Several parts of