User: ajingnk

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ajingnk130
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Posts by ajingnk

<prev • 37 results • page 1 of 4 • next >
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Answer: A: all unique compound structure (SMILES) of PubChem Database
... In case someone also needs it, PubChem has InCHI data for all compound. The FTP InCHI data can be downloaded from the following FTP directory: ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/CID-InChI-Key.gz ...
written 4.2 years ago by ajingnk130
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all unique compound structure (SMILES) of PubChem Database
... Hi everyone, I want to get all unique compound structures of PubChem Database. I have download SDF file for PubChem, but it is 45G after gzip. If I convert all SDF file to SMILES, that won't be easy... Is there any way to retrieve all SMILES for the whole PubChem?     Thanks,Jing ...
compound pubchem written 4.2 years ago by ajingnk130
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Comment: C: Is that possible to use Neighbor Joining algorithm for a distance matrix with mo
... Yes, you are right. N^2 is the best the algorithm can do. ...
written 4.2 years ago by ajingnk130
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Comment: C: Is that possible to use Neighbor Joining algorithm for a distance matrix with mo
... A tree with 1M leaf nodes is about 2M nodes and 2M edges. I was thinking to use Gephi.. But, I guess I should reduce the size of the data first. ...
written 4.2 years ago by ajingnk130
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Comment: C: Is that possible to use Neighbor Joining algorithm for a distance matrix with mo
... I need the tree structure for visualization. ...
written 4.2 years ago by ajingnk130
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Comment: C: Is that possible to use Neighbor Joining algorithm for a distance matrix with mo
... I haven't seen a popular implementation of hierarchical clustering with complexity less than N^2 ...
written 4.2 years ago by ajingnk130
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Comment: C: Is that possible to use Neighbor Joining algorithm for a distance matrix with mo
... Thanks Lars! So, RapidNJ and NINJA take care of the memory issue also? ...
written 4.2 years ago by ajingnk130
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Is that possible to use Neighbor Joining algorithm for a distance matrix with more than 1M taxa
... I have a distance matrix with more than 1M nodes. I wonder whether there exist any Neighbour Joining implementation which could calculate a tree structure within a reasonable amount of time. The complexity for Neighbour Joining is N^3, so I am not sure whether there is any heuristic algorithm could ...
tree phylo written 4.2 years ago by ajingnk130 • updated 2.8 years ago by Biostar ♦♦ 20
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Comment: C: Finding the transcript with UniProt canonical sequence (or ID)
... Thanks Elisabeth! I saw that "Sequence databases" are listed as cross-reference. Is that possible to retrieve the nucleotide sequence with sequence databases? I just want to get some rough results, so I may not need all corresponding residues. I want to know the all possible mutations for one protei ...
written 4.4 years ago by ajingnk130
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Finding the transcript with UniProt canonical sequence (or ID)
... I have UniProt canonical sequence and UniProtID. Is there any easy way (like Biopython) to get the transcript sequence for UniProt protein sequence (I also have gene name and UniProtID)? I saw many corresponding Ensemble Transcript for one UniProt entry. I just need the one corresponding to canonica ...
sequence uniprot written 4.4 years ago by ajingnk130 • updated 4.4 years ago by Elisabeth Gasteiger1.6k

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Popular Question 4.2 years ago, created a question with more than 1,000 views. For How To Plot An Unrooted Tree With Flexible Changes Of Leaf Node Size?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For How To Plot An Unrooted Tree With Flexible Changes Of Leaf Node Size?
Popular Question 5.1 years ago, created a question with more than 1,000 views. For How To Plot An Unrooted Tree With Flexible Changes Of Leaf Node Size?

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