User: guedes.aureliano

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Posts by guedes.aureliano

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Using NCBI's genomic accession to directly load GRanges in R
... Hi all, I have a simple question I'm having some difficulty to handle with. I would like to load some genomes in a GRange object (GenomicRanges package) to use the GeneNeighborhood package. The problem is, I don't know too much the BioConductor packages and I didn't find a solution to load genom ...
ncbi R granges written 27 days ago by guedes.aureliano0 • updated 13 days ago by Biostar ♦♦ 20
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Entrez progammaticly: Direct efetch or epost + efetch
... Hi all, I developed a tool in Perl to download an mount of data given entries list. The tool are working nicely at the moment. My script receive a large list of accession number and mount URL directly to efetch. Like above: my $base = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efet ...
epost efetch entrez written 2.1 years ago by guedes.aureliano0
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Comment: C: Retrieving fasta with dna sequences given prokaryotic protein accession numbers
... No, all they are associated with existing genome. Example: YP_002996579.1 I try efetch -id YP_002996579.1 -db protein -format ipg This return a list were each line is like this RefSeq NC_012891.1 854416 855570 + WP_003058145.1 spermidine/putrescine import ATP-bindin ...
written 2.9 years ago by guedes.aureliano0
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Comment: A: Retrieving fasta with dna sequences given prokaryotic protein accession numbers
... The list is 68 protein IDs from different species of Streptococcus. ...
written 2.9 years ago by guedes.aureliano0
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Retrieving fasta with dna sequences given prokaryotic protein accession numbers
... I have a list with prokaryotic proteins ACNs. Now I need to download a fasta containing the coding sequences of this proteins. I've tried efetch query for ipg format, after efetch with de genome ID with seq_start and seq_stop parameters, but the retrieve sequence isn't equal protein sequence when ...
gene retrieving sequence written 2.9 years ago by guedes.aureliano0

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Popular Question 6 months ago, created a question with more than 1,000 views. For Retrieving fasta with dna sequences given prokaryotic protein accession numbers
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Retrieving fasta with dna sequences given prokaryotic protein accession numbers

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