Difference between revisions of "Talk:Glucocerebrosidase sequence alignments"
From Bioinformatikpedia
m |
m |
||
| (2 intermediate revisions by the same user not shown) | |||
| Line 4: | Line 4: | ||
* Change the output format of Blast to give you more than 500 sequences and more than 250 details. |
* Change the output format of Blast to give you more than 500 sequences and more than 250 details. |
||
* Document how you converted the accession numbers for the HSSP comparison. |
* Document how you converted the accession numbers for the HSSP comparison. |
||
| + | * In "Comparison to HSSP" for HHsearch you should only consider the sequences with pdb structures since HHsearch only searches structures. |
||
| + | * 3D-Coffee seems to put in more rather than less gaps in the secondary structure elements. Have you investigated why this unexpected result occurs? |
||
| + | |||
| + | The term "folding" is used for the overall arrangement of structural elements (e.g. helices, etc.). So yo cannot change the "folding" without changing the entire protein. What you meant is probably "local conformation". |
||
Latest revision as of 16:22, 15 June 2011
Very nice protocol.
Some hints on what could be even nicer ;-) (You do not need to do this, just to give you feedback) :
- Change the output format of Blast to give you more than 500 sequences and more than 250 details.
- Document how you converted the accession numbers for the HSSP comparison.
- In "Comparison to HSSP" for HHsearch you should only consider the sequences with pdb structures since HHsearch only searches structures.
- 3D-Coffee seems to put in more rather than less gaps in the secondary structure elements. Have you investigated why this unexpected result occurs?
The term "folding" is used for the overall arrangement of structural elements (e.g. helices, etc.). So yo cannot change the "folding" without changing the entire protein. What you meant is probably "local conformation".
