User: fishgolden

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fishgolden450
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Posts by fishgolden

<prev • 115 results • page 3 of 12 • next >
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Comment: C: how to extract HETATM structures from pdb with python
... I think HETAM must be HETATM. ...
written 14 months ago by fishgolden450
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Answer: A: how to extract HETATM structures from pdb with python
... How did you make {sample}.csv ? Your python code has many problems. I did my best to make your code runnable. Save following 3 lines as "1hdk.csv". 1hdk,A,LEU,140 1hdk,H,PMB,929 1hdk,A,HOH,2067 and download 1hdk.pdb from https://www.rcsb.org/structure/1HDK Put those two files and ...
written 14 months ago by fishgolden450
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Answer: A: How to create PSSM matrix
... I can't see [needed format[1] and downloaded format. But do you mean that you need ascii format? You can use PSSM viewer. https://www.ncbi.nlm.nih.gov/Class/Structure/pssm/pssm_viewer.cgi Enter PSSM to view, Scoremat file -> Matrix View -> Download Matrix to File or try local psi-blas ...
written 14 months ago by fishgolden450
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Comment: C: percent identities for all by all protein alignment
... > In Clustal Omega, the alignments are then computed using the very > accurate HHalign package (Söding, 2005), which aligns two profile > hidden Markov models (Eddy, 1998). http://msb.embopress.org/content/7/1/539 It seems that Clustal Omega uses HHalign. > A distance is calculated ...
written 17 months ago by fishgolden450
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Comment: C: percent identities for all by all protein alignment
... > but other threads on the site have shown that its pairwise alignments > can be a bit janky. Oh, really. I didn't know that. Thank you for the comment. ...
written 17 months ago by fishgolden450
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Comment: C: percent identities for all by all protein alignment
... CLUSTAL and MAFFT are Multiple Sequence Alignment software that they perform stringent DP (edit: jrj.healey said CLUSTAL's alignment is a bit janky Its alignment may not be stringent one...) same as water and needle when they are used as pairwise aligner. I mean, I think CLUSTAL and MAFFT are over s ...
written 17 months ago by fishgolden450
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Answer: A: percent identities for all by all protein alignment
... > There is some sort of filtering still going on, it would appear. > Hopefully I'm just missing some parameter? > > I'd hard code it myself but I'd rather have one of these algorithms do > it for me, as they'll presumably be faster at full scale. I think this is really difficult tas ...
written 17 months ago by fishgolden450
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Comment: C: Tool suggestions for bulk domain analyses?
... Oh, sorry. I thought you have id of transcripts or genes somehow because you could do DE analysis. BTW, Pfam website accepts multiple sequences with "search"->"batch search". ...
written 18 months ago by fishgolden450
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Answer: A: Tool suggestions for bulk domain analyses?
... How about DAVID ( https://david.ncifcrf.gov/ ) or TargetMine ( https://targetmine.mizuguchilab.org/ ) ? Both have domain enrichment analysis function(s). ...
written 18 months ago by fishgolden450
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Comment: C: (solved) I couldn't reproduce the problem of max_target_seqs
... I made several dummy dbs and ran searches several times but I couldn't reproduce the problem. There are many things to consider. - How long is the length of the query sequence? - Does it contain N? - How long is the lengths of -perc_identity 99 hits? - Are they masked? - How are the alignment ...
written 18 months ago by fishgolden450

Latest awards to fishgolden

Centurion 12 months ago, created 100 posts.
Scholar 14 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Scholar 17 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Popular Question 19 months ago, created a question with more than 1,000 views. For (solved) I couldn't reproduce the problem of max_target_seqs
Supporter 21 months ago, voted at least 25 times.
Scholar 21 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Scholar 23 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Student 23 months ago, asked a question with at least 3 up-votes. For (solved) I couldn't reproduce the problem of max_target_seqs
Autobiographer 3.0 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 3.4 years ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction

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