User: anabaena

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anabaena0
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Posts by anabaena

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Finding gene matches using sequence reads?
... Awesome! So my main concern is that I have many samples to look through. The initial thought was to probe a metagenomic sample/read set and look for the gene of interest, and if present then go in an assemble reads and give the sample a deeper look. So with that being said would this pipeline be e ...
written 4 days ago by anabaena0
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Finding gene matches using sequence reads?
... Hey all, I am looking through large data sets to try and find a gene cluster or particular genes using sequence reads. The goal is to find a metagenomic set with the genes of interest, essentially just a probe to see if what I am looking for is there. Currently, I am using Bowtie2 but I was wond ...
reads bowtie2 metagenomic written 4 days ago by anabaena0 • updated 3 days ago by Fatima340
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Comment: C: Is it possible to pull Genbank ID from RefSeq?
... Awesome thanks! I am assuming these commands can be translated into Biopython? as I need to iterate over a large list? ...
written 16 days ago by anabaena0
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Is it possible to pull Genbank ID from RefSeq?
... Hey everyone, I have a list of RefSeq protein ID's and need to pull the GenkBank/INSDC data. When I pull the attached data to the RefSeq WP_XXXXX either through esummary, or elink I get no connection to anything else not even the WGS data, so I was wondering if it was even possible to do so in B ...
entrez biopython written 17 days ago by anabaena0 • updated 16 days ago by genomax78k
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Answer: A: Fetching Genbank Assembly IDs with protein
... if anyone is interested here is what I was trying to do: def find_contig_id(protein): from Bio import Entrez, SeqIO Entrez.email = 'zack.henning@berkeley.edu' print(protein) eser_handle = Entrez.efetch(id=protein, db ='protein', rettype='gb', retmode='text') ...
written 18 days ago by anabaena0
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Answer: A: assembly id from protein accession via entrez?
... If anyone is interested here is the solution to what I was trying to do: def find_contig_id(protein): from Bio import Entrez, SeqIO Entrez.email = 'xxxxxx' print(protein) eser_handle = Entrez.efetch(id=protein, db ='protein', rettype='gb', retmode='text') ...
written 18 days ago by anabaena0 • updated 18 days ago by genomax78k
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assembly id from protein accession via entrez?
... Hey all, I am trying to retrieve assembly IDs to append to a pandas dataframe. I have a BLAST output .tsv generated from an alignment with a local database I made, and what I have are the protein ascension IDs. What I need are the GenBank assembly accession IDs. When I search I can find the c ...
assembly biopython entrez written 21 days ago by anabaena0
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Comment: C: Fetching Genbank Assembly IDs with protein
... So what the end game is, is to append a pandas dataframe with the Genbank Assembly ID (i.e. GCA_XXXX.X). I ran a blast of a concatenated .faa file from thousands of assembled genomes(obtained from a BioProject) through making a local database, and do not have the assembly ID's associated the protei ...
written 24 days ago by anabaena0
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Comment: C: Fetching Genbank Assembly IDs with protein
... Alright so I am getting the WGS/contig ascencion but not the assembly ID (i.e. starts with GCA_XXXX.X). Any idea on how to retrieve that? ...
written 24 days ago by anabaena0
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Fetching Genbank Assembly IDs with protein
... Hey all, I am interested in getting records particular CDS matches. I have particular BLAST CDS matches that I need to retrieve the Genbank genome assembly ascension number. I have several hundred so I wanted to automate this with Entrez in biopython if possible. My blast results give me a pr ...
python biopython entrez written 25 days ago by anabaena0 • updated 15 days ago by vkkodali1.7k

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Scholar 18 days ago, created an answer that has been accepted. For A: assembly id from protein accession via entrez?

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