User: michau

gravatar for michau
michau20
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20
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New User
Location:
Poland/Gdansk
Last seen:
1 month, 4 weeks ago
Joined:
1 year, 6 months ago
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m***************@gmail.com

Posts by michau

<prev • 14 results • page 1 of 2 • next >
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Answer: A: How to extract a sequence from a multi-fasta file based on its position?
... python with Biopython from Bio import AlignIO N = 3 # position of seq you want to retreive with open('yourALN.fa' 'r') as infile: aln = AlignIO.read(infile, 'fasta') print(aln[N-1]) ...
written 4 months ago by michau20
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Answer: A: Multiple-Sequence Alignment Trimming
... I'm probably late with the answer, but I'll leave it anyway. The answer is No. As far as I remember (I used MEGA only on classes during my bachelor studies, and never after) this option removes all gaps which is the same as de-aligning. TrimAL removes whole columns, that are poorly aligned, or ...
written 4 months ago by michau20
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Comment: A: Handling Illumina Omni2.5 data from multiple array versions and multiple genome
... Did you have any answer (I have the same problem now) ...
written 6 months ago by michau20
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Answer: A: Remove duplicates in fasta file based on ID
... Copied from my other post: https://www.biostars.org/p/292207/#349551 Learn to use Biopython library. It's handy as hell. You can use any format as in/out > from Bio import SeqIO > > with open('output.fasta', 'a') as outFile: > record_ids = list()\ > for re ...
written 11 months ago by michau20
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Answer: A: How to remove duplicate sequences in fasta file using python?
... Learn to use Biopython library. It's handy as hell. You can use any format as in/out from Bio import SeqIO with open('output.fasta', 'a') as outFile: record_ids = list() for record in SeqIO.parse('input.fasta', 'fasta'): if record.id not in record_ids: ...
written 11 months ago by michau20
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Answer: A: How To Remove The Same Sequences In The Fasta Files?
... In Jalview (best alignment viewer) option "remove redundancy". You can select treshold. Ctrl + D or edit > remove redundancy ![jalview alignment viewer][1]+ [1]: http://www.virology.ws/wp-content/uploads/2010/10/jalview.png ...
written 11 months ago by michau20
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Answer: A: Convert Ncbi Species Names To Kegg Species Names
... If one would still land on this elderly post: There's now handy tool on uniprot website, that allows between database translations of ID. I think it covers all of them. https://www.uniprot.org/uploadlists/ ...
written 11 months ago by michau20
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Comment: C: Is there a database of phylogenetic information?
... Awesome. I was looking for this for hours. Although I was thinking more like database of published trees. Where you can browse available phylogenies for a clade you are interested in. ...
written 12 months ago by michau20
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Is there a database of phylogenetic information?
... Hi, do you know about any place to obtain up-to-date generally accepted phylogenetic trees? I need species phylogeny of Actinobacteria to measure dn/ds and I don't really want to calculate 16S nor whole-genome, because it's overkill to only workaround long branch attraction problem. Any help would ...
phylogeny databases written 12 months ago by michau20 • updated 12 months ago by 5heikki8.5k
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Comment: C: measure of residue dissimilarity in aligment (Phylogenetic discriminant)
... Firstly: Thank you for answer I was thinking to use dn/ds as a next step, but as far as I know it allows only for pairwise comparisons. I was looking for something more like measuring inside clade vs. outside clade (site specific) variation. Column-wide, like: for each column: MANOVA ...
written 12 months ago by michau20

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