User: Sishuo Wang

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Sishuo Wang50
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50
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New User
Location:
The University of British Columbia
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Google Scholar Page
Last seen:
1 month, 3 weeks ago
Joined:
4 years, 7 months ago
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Posts by Sishuo Wang

<prev • 12 results • page 1 of 2 • next >
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Comment: C: output SAM file from STAR aligner looks incomplete
... Yeah, about 30GB RAM might be required for mapping of human genome. ...
written 2.4 years ago by Sishuo Wang50
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Answer: A: Antibody Structure Prediction
... The following link might be helpful http://zhanglab.ccmb.med.umich.edu/TACOS/   Also, SWISSMODEL might work if the Combine mode or Optimize mode is chosen I think. You may need to install SwissPDB-Viewer to do this. http://swissmodel.expasy.org http://swissmodel.expasy.org/SM_Oligomer.html   ...
written 2.4 years ago by Sishuo Wang50
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Comment: C: TBLASTN on a large DNA database (352GB)
... I am not 100% sure but based on my experience it might take 10-30 mins for one sequence. ...
written 2.5 years ago by Sishuo Wang50
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Comment: C: How to obtain ancestral alleles based on Hg19 genome coordinates?
... Also, the following paper uses a ML method to infer ancestral alleles which might be more complicated than the way mentioned in the link above. http://genome.cshlp.org/content/22/12/2455.long ...
written 2.5 years ago by Sishuo Wang50
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Answer: A: How to obtain ancestral alleles based on Hg19 genome coordinates?
... The following link might be helpful I think. https://www.biostars.org/p/61267/ ...
written 2.5 years ago by Sishuo Wang50
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Answer: A: High througput BLAST-analysis
... OrthoMCL is another good choice in addition to CD-HIT as mentioned by Neilfws. Alternatively, you might want to use SiLiX which is very fast and could be used for both nucleotide sequences or amino acid sequences. ...
written 2.5 years ago by Sishuo Wang50
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Answer: A: comparing two genomes
... discontinuous megablast might also be helpful or you can change '-word_size' (=11 be default). ...
written 2.5 years ago by Sishuo Wang50
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Comment: C: Identify homolog sequences that appear in multiple RefSeq files
... OrthoMCL might be helpful. http://www.orthomcl.org/orthomcl/ It might take a long time to run the whole analysis for all of your species.   ...
written 2.6 years ago by Sishuo Wang50
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Comment: C: GenBank to fasta sequence
... from Bio import SeqIO SeqIO.convert(infile_genbank, "genbank", outfile, "fasta")   http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/genbank2fasta/ ...
written 2.6 years ago by Sishuo Wang50
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Answer: A: Species distribution in the blast output
... I think that the following script might be helpful. https://github.com/evolbeginner/taxa_search. You can extract species names from your blast output one by one and search for their detailed taxonomic information using the script. Please make sure that the package DBI is installed prior to using ...
written 2.6 years ago by Sishuo Wang50

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