User: bioguy

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bioguy30
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Posts by bioguy

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Comment: C: percent identities for all by all protein alignment
... Ah ok, thank you. Will give the others you recommended a try as well if need be. Really appreciate all the help! ...
written 5 weeks ago by bioguy30
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Comment: C: percent identities for all by all protein alignment
... Thank you – ended up going the CLUSTAL route with some basic multi-threading to speed things up. Very much appreciate your help! ...
written 5 weeks ago by bioguy30
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percent identities for all by all protein alignment
... Very simple question – I have a list of, say, 1000 protein sequences in a fasta file. I want to compute percent identities for each pair of sequences. So, in this example, it'd generated a 1000 by 1000 matrix reflected over the diagonal. I've tried diamond and blastp, but even when I set -max-targe ...
sequence alignment diamond blast written 5 weeks ago by bioguy30 • updated 5 weeks ago by fishgolden390
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Only one hit per query on blastn?
... Am trying to run blastn to check if a sequence has a similar match within a database within a certain percent identity– to speed things up, I'd like blast to stop searching after finding a single hit (it doesn't matter what the match is, just that it exists). Is there a parameter that does this? Fr ...
blast genomics written 4 months ago by bioguy30
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Comment: C: all by all phylogenetic distances for massive set of ncbi taxon ID's
... ok cool, this helps a lot, thank you. Giving it a shot now, we'll see how it works out... ...
written 5 months ago by bioguy30
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all by all phylogenetic distances for massive set of ncbi taxon ID's
... Any ideas on how to extract phylogenetic tree distances/dissimilarity for a massive group of ncbi taxonomic ids, like 50-100K? Ideally I'd be able to generate or download a file of the form: Taxa1,Taxa2,Distance Taxa1,Taxa3,Distance ...... This was the closest thing I could find (https://w ...
phylogeny ncbi taxonomy taxon id microbiology written 5 months ago by bioguy30 • updated 5 months ago by i.sudbery4.8k
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Answer: A: extract EC number from entrez esearch query
... Excellent, thank you. Alternative method I just found: esearch -db 'protein' -query 'RRJ88579.1' | efetch -format gpc | xtract -insd Protein EC_number ...
written 6 months ago by bioguy30
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extract EC number from entrez esearch query
... Anyone have any idea how to use NCBI's entrez command line (https://www.ncbi.nlm.nih.gov/books/NBK25501/) to extract feature information about a specific protein query? Specifically, I need to find ECid's for given queries. For example, if I want to programmatically access the ECID for the followin ...
ncbi protein entrez genomics ecid written 6 months ago by bioguy30
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a mapping between ncbi taxonomy ID and habitat?
... Am trying to find a database mapping between bacterial taxonomy ID and where that microbe is likely to be isolated from (ie human gut, soil, plants, etc). Tried JGI-Gold but have had little success with consistency of annotation quality + accuracy. Any ideas? ...
genome microbiology written 7 months ago by bioguy30

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Scholar 6 months ago, created an answer that has been accepted. For A: extract EC number from entrez esearch query

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