Difference between revisions of "Talk:Gaucher Disease: Task 02 - Alignments"
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Kalemanovm (talk | contribs) |
Kalemanovm (talk | contribs) |
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| − | TODO: |
+ | TODO (task 1): |
| − | * Add number of hits only after big_80 iterations into the table |
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| − | * Move all methods used into "lab journal" page for the task |
||
| − | * Explain about checkpoint files in Psi-BLAST |
||
* Look at same hits in HHblits and Psi-BLAST: what E-values do they have? |
* Look at same hits in HHblits and Psi-BLAST: what E-values do they have? |
||
* Analyse the hits that overlap for both and those which are only found in one of the programs (distributions, evaluation) |
* Analyse the hits that overlap for both and those which are only found in one of the programs (distributions, evaluation) |
||
| + | |||
| + | done: (task 1) |
||
| + | * Maybe an error in Psi-BLAST runs, because all results are the same --> no, only in the first iteration against big the number of hits is the same, but not in the second (--> added in the table) and not after pdb search (also the profiles are different). |
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| + | * Move all methods used into "lab journal" page for the task |
||
* Write down with which versions (dates) of the databases we worked |
* Write down with which versions (dates) of the databases we worked |
||
| + | - Big & Big_80 (/mnt/project/rost_db/data/big/big[_80]): before 30 Apr 2013? -> Big is updated with delay, especially on the student cluster! |
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- Uniprot_20 (/mnt/project/rost_db/data/hhblits/uniprot_20): 02 Sep 2011 -> now Feb13 is available online! |
- Uniprot_20 (/mnt/project/rost_db/data/hhblits/uniprot_20): 02 Sep 2011 -> now Feb13 is available online! |
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| − | - Big & Big_80 (/mnt/project/rost_db/data/big/big[_80]): before 30 Apr 2013? -> Big is updatet with delay, especially on the student cluster! |
||
- pdb_seqres (/mnt/home/rost/kloppmann/data/blast_db/pdb_seqres): 3 May 2013 |
- pdb_seqres (/mnt/home/rost/kloppmann/data/blast_db/pdb_seqres): 3 May 2013 |
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| − | - pdb_full (mnt/project/rost_db/data/hhblits/pdb_full): before 30 Apr 2013? |
+ | - pdb_full (/mnt/project/rost_db/data/hhblits/pdb_full): before 30 Apr 2013? |
- COPS (/mnt/project/pracstrucfunc13/data/COPS/COPS-ChainHierarchy.txt): 27 Apr 2012 |
- COPS (/mnt/project/pracstrucfunc13/data/COPS/COPS-ChainHierarchy.txt): 27 Apr 2012 |
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*Software sharing: copy paste the code |
*Software sharing: copy paste the code |
||
**share the evaluation script |
**share the evaluation script |
||
| + | * Explain about checkpoint files in Psi-BLAST (in "lab journal") |
||
| − | |||
| + | * Add number of hits only after big_80 iterations into the table |
||
| − | done: |
||
| − | * Maybe an error in Psi-BLAST runs, because all results are the same --> no, only in the first iteration against big the number of hits is the same, but not in the second (--> added in the table) and not after pdb search (also the profiles are different). |
||
Latest revision as of 13:13, 21 May 2013
TODO (task 1):
- Look at same hits in HHblits and Psi-BLAST: what E-values do they have?
- Analyse the hits that overlap for both and those which are only found in one of the programs (distributions, evaluation)
done: (task 1)
- Maybe an error in Psi-BLAST runs, because all results are the same --> no, only in the first iteration against big the number of hits is the same, but not in the second (--> added in the table) and not after pdb search (also the profiles are different).
- Move all methods used into "lab journal" page for the task
- Write down with which versions (dates) of the databases we worked
- Big & Big_80 (/mnt/project/rost_db/data/big/big[_80]): before 30 Apr 2013? -> Big is updated with delay, especially on the student cluster! - Uniprot_20 (/mnt/project/rost_db/data/hhblits/uniprot_20): 02 Sep 2011 -> now Feb13 is available online! - pdb_seqres (/mnt/home/rost/kloppmann/data/blast_db/pdb_seqres): 3 May 2013 - pdb_full (/mnt/project/rost_db/data/hhblits/pdb_full): before 30 Apr 2013? - COPS (/mnt/project/pracstrucfunc13/data/COPS/COPS-ChainHierarchy.txt): 27 Apr 2012
- Software sharing: copy paste the code
- share the evaluation script
- Explain about checkpoint files in Psi-BLAST (in "lab journal")
- Add number of hits only after big_80 iterations into the table
