User: fishgolden

gravatar for fishgolden
fishgolden420
Reputation:
420
Status:
Trusted
Location:
Last seen:
12 hours ago
Joined:
2 years, 8 months ago
Email:
k***************@gmail.com

-_-

Posts by fishgolden

<prev • 101 results • page 1 of 11 • next >
0
votes
2
answers
75
views
2
answers
Answer: A: biopython.PDB residue.get_id() does not match sequence index
... I'm not using biopython but as I thought this is one of the general pit fall of handling PDB structure, I give an answer. (please give a comment if it isn't) Why idx and id are different is because "id" means not "index" but "identifier". Residues in PDB have several ids. There are two such ids at ...
written 19 days ago by fishgolden420
1
vote
3
answers
648
views
3
answers
Comment: C: Multiple alignment software
... They are amino acid sequences thus they must be reverse translated into nucleotide when you benchmark nucleotide alignment software. Then it becomes codon-based alignment benchmark (the gaps are placed between two codon frames. It's quite biased.) & It can not be applied to aligning SINE. ...
written 4 weeks ago by fishgolden420
0
votes
3
answers
648
views
3
answers
Comment: C: Multiple alignment software
... https://www.ncbi.nlm.nih.gov/pmc/articles/PMC29792/ BaliBASE is from proteins which have 3D structure... Nucleotide people may use it for benchmarking algorithms, however, it's not suitable for his analysis, at least.... ...
written 4 weeks ago by fishgolden420
0
votes
1
answer
154
views
1
answers
Comment: C: Local protein BLAST not working
... Isn't it that you should give to "query=" arg, instead of raw amino acid sequence? ...
written 4 weeks ago by fishgolden420
1
vote
3
answers
648
views
3
answers
Answer: A: Multiple alignment software
... At a glance, I thought that all alignments are nonsense. I wouldn't do any downstream analysis with any of those alignments. However, if you want to discuss about the accuracy of algorithms; T-Coffee, Clustal Omega, and yours, you should evaluate those algorithms with some benchmark dataset. I'm ...
written 5 weeks ago by fishgolden420
0
votes
1
answer
193
views
1
answers
Comment: C: How to create PSSM matrix
... "I have downloaded this as a pssm" It's ASN.1 format. You can use it as input file of sofware/web-service in my answer. I can't see needed format[1] yet. ...
written 5 weeks ago by fishgolden420
0
votes
2
answers
269
views
2
answers
Comment: C: how to extract HETATM structures from pdb with python
... I think HETAM must be HETATM. ...
written 8 weeks ago by fishgolden420
1
vote
2
answers
269
views
2
answers
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 8 weeks ago by fishgolden420
0
votes
1
answer
193
views
1
answers
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 11 weeks ago by fishgolden420
0
votes
2
answers
256
views
2
answers
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 5 months ago by fishgolden420

Latest awards to fishgolden

Centurion 19 days ago, created 100 posts.
Scholar 8 weeks ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Scholar 5 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Popular Question 7 months ago, created a question with more than 1,000 views. For (solved) I couldn't reproduce the problem of max_target_seqs
Supporter 9 months ago, voted at least 25 times.
Scholar 9 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Scholar 11 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Student 11 months ago, asked a question with at least 3 up-votes. For (solved) I couldn't reproduce the problem of max_target_seqs
Autobiographer 2.0 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.4 years ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1327 users visited in the last hour