User:Eric Martz/Sandbox 13

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Sequence Alignment Tools

What I want:

  1.  % identity vs. length of each chain and number of identical residues/chain length for each chain
  2. colors that indicate identity/similarity/difference
  3. ability to block a region of the alignment and get identity and length for that region (could cut and paste a new job ...)

Jalview: seems to be mostly an alignment editing tool.

EBI Clustal

RCSB Compare Structures: Smith-Waterman or Needleman-Wunsch does #1,#2 but only for sequences of 3D structures. Smith-Waterman shows only the aligned segments, while Needleman-Wunsch shows full length with gaps.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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