SEgment Alignment (SEA) server

(Protein pairwise alignment based on network matching algorithm)

Documents: algorithm paper; a presentation; benchmarking

Yuzhen Ye, Lukasz Jaroszewski, Weizhong Li, and Adam Godzik. A segment alignment approach to protein comparison. Bioinformatics 2003 19: 742-749 Abstract Paper
Dariusz M Plewczynski , Leszek Rychlewski , Yuzhen Ye , Lukasz Jaroszewski and Adam Godzik. Integrated web service for improving alignment quality based on segments comparison BMC Bioinformatics 2004, 5:98 Abstract Paper

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Sequences in fasta format or pure sequences are required
Browse first sequence file:
Or paste your sequence
Browse second sequence file:
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  • Fragment prediction (current SEA server only uses structure segments from FRAGlib).
    • Cut-off value on the scores of fragments ([-2.0, 0]):
  • Alignment options
    • Alignment model (local or global alignment):
      Weight of local structure similarity ([0-1]):
      Gap creating penalty: ; Gap extension penalty:
  • Outputs list
    • Local structure fragment predictions in raw format(example).
      Local structure fragment predictions in html format(example).
      Sequence alignment along with predicted local structures (example).
      Sequence alignment in fasta format.
      Alignment graph(example).
      Graphic showing of structure segments predicted by FRAGlib and those selected by SEA(example).

Please contact Yuzhen Ye if you have questions about SEA
or Dariusz Plewczynski if you have questions about FRAGlib
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Godzik Laboratory, The Burnham Institute

First set up Apr, 2003
Latest maintenance July 26, 2004

This project is supported by SPAM grant (GM63208)