Moderator: 5heikki

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5heikki6.5k
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Posts by 5heikki

<prev • 933 results • page 1 of 94 • next >
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Comment: C: Use machine learning as classifier
... Blast is bad algorithm for this stuff. Try the RDP classifier from their github. You can get species level classification with it as long as you have a species level map file.. ...
written 13 days ago by 5heikki6.5k
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Comment: C: Use machine learning as classifier
... Oftentimes even full 16S doesn't offer enough resolution for species level classification.. ...
written 13 days ago by 5heikki6.5k
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Answer: A: converting lowercase letters to uppercase letters in fasta file
... Field separator is space, if line doesn't begin with ">" output uppercase, else output first field as is. awk 'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $1}}' in.fna > out.fna ...
written 15 days ago by 5heikki6.5k
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Comment: C: grep chromosome on blast result
... How about: man grep ...
written 15 days ago by 5heikki6.5k
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Comment: C: Expand a DNA sequence with IUPAC codes into multiple sequence in R
... All this stuff is well documented, [seq][1] & [itertools][2]. [1]: http://biopython.org/DIST/docs/api/Bio.Seq.Seq-class.html [2]: https://docs.python.org/2/library/itertools.html ...
written 15 days ago by 5heikki6.5k
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Answer: A: Expand a DNA sequence with IUPAC codes into multiple sequence
... This is super easy with Python, see e.g. [here][1]. Copy pasted one option below: from Bio import Seq from itertools import product def extend_ambiguous_dna(seq): """return list of all possible sequences given an ambiguous DNA input""" d = Seq.IUPAC.IUPACData.ambiguo ...
written 17 days ago by 5heikki6.5k
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Comment: C: [Blastn]Alignment result changes after using -max_target_seqs option
... *I assumed that this means that only the TOP ten alignment result would be stored into the resulted testing file.* -max_target_seqs =1> Maximum number of aligned sequences to keep Not applicable for outfmt <= 4 Note, maximum number of aligned sequences, not maximum number ...
written 17 days ago by 5heikki6.5k
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Answer: A: Editing header of a fasta file
... cut -f1 -d ":" in.fa > out.fa edit. nevermind, thought you wanted the first "field".. ...
written 22 days ago by 5heikki6.5k
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Comment: C: Retrieve genbank viral genomes
... viral.1.1 & viral.2.1 contain entries such as: >ref|NC_021094.1| White clover cryptic virus 2 isolate IPP_Lirepa segment RNA 1, complete sequence >ref|NC_021095.1| White clover cryptic virus 2 isolate IPP_Lirepa segment RNA 2, complete sequence >ref|NC_021096.1| Red clover ...
written 23 days ago by 5heikki6.5k
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Comment: C: Amd Or Intel Based Workstation For Bioinformatics?
... Replying to a very old post.. dual socket setups are Xeon only. Anyway, we're living interesting times and it sure seems like AMD's threadripper CPU's are the obvious choice right now.. ...
written 24 days ago by 5heikki6.5k

Latest awards to 5heikki

Scholar 10 days ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 7 weeks ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 7 weeks ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 3 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Scholar 3 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 5 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Popular Question 5 months ago, created a question with more than 1,000 views. For Are old versions of NCBI's nr stored somewhere?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: fasta header with leading zeros
Popular Question 6 months ago, created a question with more than 1,000 views. For Are old versions of NCBI's nr stored somewhere?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: fasta header with leading zeros
Scholar 7 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Common name to latin/scientific name converter

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