3bsqA Methods & Materials: Difference between revisions
No edit summary |
No edit summary |
||
| Line 2: | Line 2: | ||
The crystal structure of all proteins involved (ASA, ASK and STS) were viewed using the protein data bank text file, downloaded to the '''PyMol''' (Downloaded version in 'colaborative learning center' (CLC)). | The crystal structure of all proteins involved (ASA, ASK and STS) were viewed using the protein data bank text file, downloaded to the '''PyMol''' (Downloaded version in 'colaborative learning center' (CLC)). | ||
The structural alignment was done using the [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 DALI server] with PDB identifiers. | The structural alignment was done using the [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 DALI server] with PDB identifiers. | ||
Protein interaction of ASK were searched with the programme [http://string.embl.de/ STRING]which is available online. | Protein interaction of ASK were searched with the programme [http://string.embl.de/ 'STRING']which is available online. | ||
The protein name or PDB identifier was not detected by 'STRING', therefore the aminoacid sequence was used. | The protein name or PDB identifier was not detected by 'STRING', therefore the aminoacid sequence was used. | ||
Functions of selected proteins were searched using '''ProFunc''', which is freely available online. | Functions of selected proteins were searched using '''ProFunc''', which is freely available online. | ||
'Two sequence alignment' of ASK and STS was done with the programme '''SIM'''. The methode used was 'BLOSUM62'. A 'gap penalty' of 5 and 'gap extension penalty' of 2 were used to optimise the alignment according to what was observed in 'clustalX'. | 'Two sequence alignment' of ASK and STS was done with the programme '''SIM'''. The methode used was 'BLOSUM62'. A 'gap penalty' of 5 and 'gap extension penalty' of 2 were used to optimise the alignment according to what was observed in 'clustalX'. | ||
The pylogenic tree was made using the 'clusalX' alignment and viewed with '''Treeview''' from the DVD. | The pylogenic tree was made using the 'clusalX' alignment and viewed with '''Treeview''' from the DVD. | ||
Revision as of 04:38, 7 June 2008
Multiple sequence alugnment was made using clustalX from the DVD. The crystal structure of all proteins involved (ASA, ASK and STS) were viewed using the protein data bank text file, downloaded to the PyMol (Downloaded version in 'colaborative learning center' (CLC)). The structural alignment was done using the DALI server with PDB identifiers. Protein interaction of ASK were searched with the programme 'STRING'which is available online. The protein name or PDB identifier was not detected by 'STRING', therefore the aminoacid sequence was used. Functions of selected proteins were searched using ProFunc, which is freely available online. 'Two sequence alignment' of ASK and STS was done with the programme SIM. The methode used was 'BLOSUM62'. A 'gap penalty' of 5 and 'gap extension penalty' of 2 were used to optimise the alignment according to what was observed in 'clustalX'. The pylogenic tree was made using the 'clusalX' alignment and viewed with Treeview from the DVD.
