User: Sishuo Wang
Sishuo Wang • 50
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- Location:
- The University of British Columbia
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- Google Scholar Page
- Last seen:
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- Joined:
- 4 years, 7 months ago
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Posts by Sishuo Wang
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... Yeah, about 30GB RAM might be required for mapping of human genome.
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written 2.4 years ago by
Sishuo Wang • 50
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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
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written 2.4 years ago by
Sishuo Wang • 50
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... I am not 100% sure but based on my experience it might take 10-30 mins for one sequence.
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written 2.5 years ago by
Sishuo Wang • 50
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... 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
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written 2.5 years ago by
Sishuo Wang • 50
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... The following link might be helpful I think.
https://www.biostars.org/p/61267/
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written 2.5 years ago by
Sishuo Wang • 50
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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.
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written 2.5 years ago by
Sishuo Wang • 50
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Answer:
A: comparing two genomes
... discontinuous megablast might also be helpful or you can change '-word_size' (=11 be default).
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written 2.5 years ago by
Sishuo Wang • 50
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... 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.
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written 2.6 years ago by
Sishuo Wang • 50
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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/
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written 2.6 years ago by
Sishuo Wang • 50
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... 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 Wang • 50
Latest awards to Sishuo Wang
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2.5 years ago,
voted at least 25 times.
Popular Question
3.4 years ago,
created a question with more than 1,000 views.
For Which software can be used to visualize phylogenetic trees with a large number of OTUs (e.g. 50,000)
Student
3.8 years ago,
asked a question with at least 3 up-votes.
For Which software can be used to visualize phylogenetic trees with a large number of OTUs (e.g. 50,000)
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