User: Chris

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Chris1.6k
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Location:
Munich
Website:
http://www.rostlab.org...
Last seen:
5 years, 10 months ago
Joined:
8 years, 3 months ago
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Researcher in structural bioinformatics

Posts by Chris

<prev • 80 results • page 1 of 8 • next >
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Answer: A: Clustering Large Dataset In Terms Of Sequence Similarity Using Eg... Blastclust
... Have a look at CD-HIT [1]. Should take only minutes for that much sequences to cluster. [1] http://weizhong-lab.ucsd.edu/cd-hit/ ...
written 5.9 years ago by Chris1.6k
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Answer: A: Blastpgp_Mutant_Residue
... What is it you want to achieve? A common scenario is: Given a protein sequence and a mutation in the form wtposmt (e.g. M1D), what are the PSSM values for M and D at position 1? To answer that question you have to psi-blast your sequence against a sequence database and parse the PSSM matrix for thos ...
written 5.9 years ago by Chris1.6k
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Comment: C: Mapping Uniprot To Ensembl Genes
... True, the Ensembl reference for Q9Y5I3 seems to have vanished during last SwissProt's update, i.e. I cannot find it either anymore, strange. ...
written 6.0 years ago by Chris1.6k
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Answer: A: Mapping Uniprot To Ensembl Genes
... As usual, when it comes to mappings between uniprot and external ids, the most reliable approach is to look into the Trembl/SwissProt flatfiles and parse for the uniprot accession and the desired external accession. Uniprot acc is listed in the AC field, external ones are within the DR fields. So in ...
written 6.0 years ago by Chris1.6k
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Answer: A: How Do I Get A Proper Prediction With Libsvm?
... Your set containing the instances to be predicted needs to be in exactly the same format as the training data. This means it needs a leading (dummy) class label (set it to 1) per instance, and the feature values per instance have to be preceded by a running number that reflects the feature number pl ...
written 6.0 years ago by Chris1.6k
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Answer: A: Map Gi Numbers To Go Codes
... Have a look at the SwissProt flatfile. It contains both GO(s) and GI for a given protein. ...
written 6.0 years ago by Chris1.6k
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Comment: C: Is There Any File That Links The Enzyme Comission Number To Gi Numbers?
... This one is contained in TrEMBL, the other (bigger) part of Uniprot. You'll find its flatfile at the same URL as the uniprot_sprot file. ...
written 6.0 years ago by Chris1.6k
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Comment: C: Is There Any File That Links The Enzyme Comission Number To Gi Numbers?
... Here you go: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz ...
written 6.0 years ago by Chris1.6k
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Answer: A: Is There Any File That Links The Enzyme Comission Number To Gi Numbers?
... The SwissProt flat file contains those data. The EC number could be found in the DE field, the GI (gene identifier) in one of the DR lines. An example could be found e.g. in the entry 3HAO_RALME. ...
written 6.0 years ago by Chris1.6k
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Answer: A: Find Similar Substructures For A Given Protein
... I would approach this by using a distance matrix-based method. First, translate your substructure into a distance matrix, i.e. calculate all pairwise C-alpha atoms distances. Second, represent each PDB structure as a distance matrix. Third, 'slide' your substructure-matrix over each PDB distance mat ...
written 6.0 years ago by Chris1.6k

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