Talk:Gaucher Disease: Task 02 - Alignments

From Bioinformatikpedia

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
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