Composition Alignment Tool

Sequence One in FASTA Format:	Use reverse complement

Sequence Two in FASTA Format:	Use reverse complement

Alignment Type and Parameters:

Compositional Local Sequence To Sequence

k-best

Alignment Type:

Nucleotides

Dinucleotides

limit

Alignment Parameters:

match score
cost of mismatch
cost of gap/insert

Match Functions:

Function 1

Function 2

Function 3

Function 4

Function 5

Function 6

Compositional Global Sequence To Sequence

Compositional Global Pattern To Local Sequence

Which is Pattern:

Sequence One

Sequence Two

Matching Functions Legend:

Function 1: The simplest function, a constant times the length of the match.

Function 2: Square root of length of extended match times a constant.

Function 3: Log base 2 of length+1 of extended match times a constant.

Function 4: Relative entropy of substring composition with respect to background composition times length of extended match times a constant.

Function 5: Relative entropy of substring composition with respect to background composition times length of extended match times a constant. For length =1, normal match value prevents two identical sequences composed of only one letter from scoring zero if the background is the same letter.

Function 6: Shannon-Jensen entropy of substring composition versus the background composition times length of extended match times a constant.