User:Eric Martz/Sandbox 13
From Proteopedia
(Difference between revisions)
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# ability to block a region of the alignment and get identity and length for that region (could cut and paste a new job ...) | # 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. | ||
| - | + | == Jalview == | |
| + | Seems to be mostly an alignment ''editing'' tool. | ||
| - | RCSB Compare Structures | + | |
| + | == ClustalW2 at EBI == | ||
| + | [http://www.ebi.ac.uk/Tools/msa/clustalw2/ ClustalW2] | ||
| + | *has colors but no color key | ||
| + | *no % id (?!) | ||
| + | *give a ''score'' but doesn't explain it. | ||
| + | |||
| + | |||
| + | |||
| + | == 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. | ||
| + | |||
| + | Swiss-Model | ||
| + | |||
| + | Why doesn't it make a model of FlgE CamJe using 1wlg? | ||
Revision as of 05:56, 25 May 2011
Sequence Alignment Tools
What I want:
- % identity vs. length of each chain and number of identical residues/chain length for each chain
- colors that indicate identity/similarity/difference
- 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.
ClustalW2 at EBI
- has colors but no color key
- no % id (?!)
- give a score but doesn't explain it.
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.
Swiss-Model
Why doesn't it make a model of FlgE CamJe using 1wlg?
