User:Eric Martz/Sandbox 13: Difference between revisions
Jump to navigation
Jump to search
Jalview
ClustalW2 at EBI
RCSB Compare Structures
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| Line 6: | Line 6: | ||
# 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. | |||
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 08:56, 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 ...)
JalviewJalview
Seems to be mostly an alignment editing tool.
ClustalW2 at EBIClustalW2 at EBI
- has colors but no color key
- no % id (?!)
- give a score but doesn't explain it.
RCSB Compare StructuresRCSB 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?