User: gb

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gb280
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Posts by gb

<prev • 60 results • page 1 of 6 • next >
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Answer: A: Blast With Biopython
... Something like this: cline = NcbiblastnCommandline(query="m_cold.fasta", db="nt", strand="plus",evalue=0.001, out="m_cold.xml", outfmt=5) Or: cline = NcbiblastnCommandline(query="m_cold.fasta", db="nt", strand="minus",evalue=0.001, out="m_cold.xml", outfmt=5) With the strand parameter y ...
written 3 days ago by gb280
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Comment: C: Blast With Biopython
... Standalone blast or online? ...
written 7 days ago by gb280
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Comment: C: Metagenomics community profiling approaches.
... "Marker gene based method are biased" True, if you do amplicon sequencing and a PCR. But you have a metagenome as I understand from your question. You can not just use any gene to find the taxonomy. Maybe metaphlan can help: http://huttenhower.sph.harvard.edu/metaphlan ...
written 11 days ago by gb280
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Comment: C: Metagenomics community profiling approaches.
... I do not have an answer, but should you not only use certain markers to find the taxonomy? Markers like CO1, 16S, 18S, ITS etc. Because you say you the whole metagenome. There are genes that are in almost every organism so just take a random taxonomy would not be good. ...
written 11 days ago by gb280
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Comment: C: Replace Accesion Headers by full ncbi Lineage Taxnomy
... The NCBI taxonomy always works in combination with the tax ID. I use the files merged.dmp and rankedlineage.dmp from here ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.zip and ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz. ...
written 15 days ago by gb280
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Comment: C: Insertion and Deletion representation in a sequence alignment
... How else you could represent it? And which kind of alignment do you mean? Never saw that the length influence the penalty ...
written 22 days ago by gb280
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Answer: A: Simple visual output of Pairwise Sequence alignment
... When I read plasmid and visualization I think off circos. http://circos.ca/ ...
written 23 days ago by gb280
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Comment: C: How to update nr database for commandline BLAST?
... In the terminal: cpan -i Archive::Tar Also check your perl version: perl -v ...
written 25 days ago by gb280
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Comment: C: accessing variable value outside the function
... Let us know if you have problems ...
written 25 days ago by gb280
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Comment: C: How to update nr database for commandline BLAST?
... For now I would say, just remove everything and execute the update script. I thought it already was that it downloads new files and also update. You always need to update everything. you may need to update your perl. https://stackoverflow.com/questions/47801223/how-to-fix-cant-locate-archive-tar-pm ...
written 25 days ago by gb280

Latest awards to gb

Scholar 11 days ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Appreciated 27 days ago, created a post with more than 5 votes. For A: Removing Duplicates before aligning
Scholar 27 days ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 6 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples

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