XSTREAM Web Interface




XSTREAM is a rapid and powerful algorithm for identifying perfect and degenerate tandem repeat motifs in protein (and nucleotide) sequence data. XSTREAM also effectively models the architecture of repetitive domains in tandem repeat proteins and eliminates motif redundancy to identify "fundamental" tandem repeat patterns.

Please acknowledge XSTREAM in your publications by citing: BMC Bioinformatics (2007) 8:382.












Options


TR Degeneracy TR Significance

Sequence Type TR Block Schematic
Min Word Match (i) Min Consensus Match (I)
Min Period (minP) Max Period (maxP)
Min Copy No. (minC) Max Gaps (g)
Min Domain Length (minD) Min TR Content [0-1]

More Settings


Output Format:
Colored Character Output True False

Seed Extension:
Short Seed Length
Medium Seed Length
Max Seed Length

Dynamic Programming:
Match Score
Miss Penalty
Gap Penalty

Consensus Error:
Max Indel Error
Consecutive Gap Max (g*)

Merging:
Do Merging True False
Max Period Breadth
Max Non-overlap Space
Max Non-overlap Period Fraction

Redundancy Removal:
Output Redundancy Filter True False
Alpha
Beta
Gamma
Delta

TR Detection:
Divide and Conquer True False
Look for Nested TRs True False
2-Stage Period Threshold (T)
Long Period Filter (t)

TR Clustering:
Do Consensus Comparison True False