User: sunyeping

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sunyeping30
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Posts by sunyeping

<prev • 13 results • page 1 of 2 • next >
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how to automatically split mol2 file containing multiple ligands
... Dear Biostars users, I wish to do some virtual screening with autodock 4. I have split a sdf file contains over a thousand compounds into single mol2 file. However, I find lots of such mol2 files still contain multiple ligands whose coordinates mix together and so can not be split by shell command ...
virtual screening autodock written 4 months ago by sunyeping30
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How to use mafft to do large scale sequence alignment?
... I wish to use mafft to do sequence alignment on a large protein sequence dataset which contains over 100,000 sequences with average sequence length being 1000 residues. I guess I need to use a supercomputer. Does anyone know how many CPU cores and how large memory does it need to run the alignment ...
alignment written 11 months ago by sunyeping30 • updated 11 months ago by Cupton70
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cuda-accelerated sequence alignment program
... Dear all, I want to do protein sequence alignment with a very large dataset which contains over 130,000 sequences. Could you recommend some cuda-accelerated sequence alignment software? I find there is a cuda-mafft, the cuda-accelerated mafft, but I don't know where to download the code. Do you kno ...
alignment written 11 months ago by sunyeping30
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Aliview cannot read large sequence file?
... Dear all I am trying to load a sequence fasta file into aliview in centos 7 system. The fasta file (74.5 MB) contains over 270,000 protein sequences with the length of each sequence being 1400 residues. I use the File>open file menu of aliview to open the file, but nothing is loaded into the ali ...
sequence written 11 months ago by sunyeping30
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Comment: C: How to prepare high-resolution protein secondary structures diagrams?
... Among the outputs of Procheck, the "residue properties plot" contains the secondary structure information and that is useful. Thank you. ...
written 12 months ago by sunyeping30
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Comment: C: How to prepare high-resolution protein secondary structures diagrams?
... PSIPRED predict secondary structures from sequence. What I need is to plot secondary structures diagrams from pdb file. ...
written 12 months ago by sunyeping30
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How to prepare high-resolution protein secondary structures diagrams?
... Dear everyone, I would like to prepare some protein secondary structures diagrams. I know that I can do this by uploading my pdb file to the pdbsum server (http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.plpdbcode=index.html) which produces the econdary structure diagrams lik ...
gene written 12 months ago by sunyeping30 • updated 12 months ago by Mensur Dlakic6.0k
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Comment: C: Where can I get promotif?
... The two email address are also inaccessible. All emials I wrote to them were returned with the complaint that these email addresses do not exit. ...
written 13 months ago by sunyeping30
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Where can I get promotif?
... Dear all, I would like to draw protein topology with promotif. According to the introduction of promotif online (http://www.img.bio.uni-goettingen.de/ms-www/internal/manuals/promotif/promotif.html), it is available from the ftp server (IP address 128.40.46.11) , but I cannot open the website with ...
protein structure written 13 months ago by sunyeping30 • updated 13 months ago by jgreener240
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How to download the sequences of a gene of all species?
... Dear everyone, How do you download the sequences of a gene of all species? For example, dUTPase is an enzyme existing in almost all organisms. How to download the coding DNA sequences of dUTPase of all organisms? I searched GenBank with the keyword "dUTPase" and it returned 73570 results. Many of t ...
sequence written 14 months ago by sunyeping30 • updated 14 months ago by MatthewP680

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