User: sunyeping

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sunyeping30
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1 year, 4 months ago
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Posts by sunyeping

<prev • 12 results • page 1 of 2 • next >
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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 21 days ago by sunyeping30 • updated 12 days ago by Cupton40
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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 26 days 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 26 days 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 5 weeks 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 5 weeks 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 5 weeks ago by sunyeping30 • updated 5 weeks ago by Mensur Dlakic1.3k
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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 3 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 3 months ago by sunyeping30 • updated 3 months ago by jgreener100
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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 4 months ago by sunyeping30 • updated 4 months ago by MatthewP260
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How to deal with gaps during translation with biopython
... I need to translate aligned DNA sequences with biopython from Bio.Seq import Seq from Bio.Alphabet import generic_dna seq = Seq("tt-aaaatg") seq.translate() Running this script will get error: Bio.Data.CodonTable.TranslationError: Codon 'TT-' is invalid. Is there a way to translat ...
sequence written 4 months ago by sunyeping30 • updated 4 months ago by rando220

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