Difference between revisions of "Help:Sequencing Tool:Automatic Assessment Algorithm"

(Explanation of the automatic sequencing algorithm)
 
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Reverse Sequence - The reverse compliment of a sequence read that extended from right-to-left along a target part.
 
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.
 
The sequencing program converts all raw sequences to either forward or reverse sequences based on the primer used.
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===New Sequences===
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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:
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The BioBrick Prefix
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===Best Matching Sequences===
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Several parts of
  
 
===Aligning Sequences===
 
===Aligning Sequences===

Revision as of 18:50, 19 March 2008

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

Aligning Sequences