User: pawlowac

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pawlowac60
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Posts by pawlowac

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Question about searching for/manipulating FASTA sequences in Biopython
... I've recently learned how to use biopython, and python for that matter. Sometimes I found myself overthinking the problem I had, and thought it was a biology problem. There is a much easier way to approach this by string matching. If the '__' is conserved, you could split the name at that point, and ...
written 20 months ago by pawlowac60 • updated 20 months ago by WouterDeCoster35k
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Answer: A: Using E-Utilities/Entrez/Elink to access identical proteins
... It appears I was approaching the question wrong. You don't need to 'link' to the identical protein list, despite the 'protein_protein_identical' link name, and description [here][1] on the NCBI website. Instead, it is information intrinsic to each accession number. epost_1 = Entrez.read(Entre ...
written 22 months ago by pawlowac60
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Comment: C: Using E-Utilities/Entrez/Elink to access identical proteins
... Also, I am aware of https://www.biostars.org/p/168331/. However, I need to make thousands of requests, and this doesn't seem the most succinct method for doing so and takes longer. ...
written 22 months ago by pawlowac60
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Answer: A: MAFFT branch length VS. BLAST
... MAFFT isn't made for multiple genome alignments, particularly because of horizontal gene transfer and rearrangements (assuming this occurs for what you are looking at). Also, MAFFT guide tree and a pairwise blast identity are very very different things, and the MAFFT guide tree is not a phylogenetic ...
written 22 months ago by pawlowac60
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Using E-Utilities/Entrez/Elink to access identical proteins
... I'm trying to access identical protein information for a list of protein accession numbers. My goal it to take protein ID's, get identical protein list, use the nucleotide coordinates from that list to specifically download the upstream and downstream region of a given gene. I was hoping to use the ...
ncbi biopython genbank entrez written 22 months ago by pawlowac60
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Help: do I always have to re-open sequence file within a for loop in python?
... I'm trying to extract nucleotide sequences from a draft genome based on alignment coordinates from a SAM file. Right now, I'm opening the SAM file as a csv, then matching sequence name and finally grabbing the sequence based on the coordinates. import csv import re from Bio import SeqIO bam_file= ...
python bowtie2 sam biopython written 2.9 years ago by pawlowac60 • updated 2.8 years ago by Peter5.7k
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Answer: A: Getting species name after doing blastx?
... Blastx results should contain accession numbers. Extract those (using tabular output, I think you can open in excel and copy and paste the column with accessions) to a text file (1 per line) and submit it to batch entrez. From there, use the 'Sent to' option to download summary files for every acces ...
written 3.4 years ago by pawlowac60
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Answer: A: Good Journals for publishing biological database paper
... Depending on the function of your enzymes, it could be sent to a field specific journal. For example, PMID 23650175. ...
written 3.4 years ago by pawlowac60
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Comment: C: Submitting several BLAST queries using NCBIWWW at once
... Unfortunately I need the diversity and there is significant overlap in results between the sequences. I end up parsing the XML results using biopython and grabbing sequence ID with certain conditions and then check for duplicates before using efetch to grab FASTA files. Oh well, back to the drawing ...
written 3.7 years ago by pawlowac60
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Comment: C: Submitting several BLAST queries using NCBIWWW at once
... Ok, I take it back. It worked once, but now it says CPU limit exceeded. There was 150 proteins I was trying to blast... ...
written 3.7 years ago by pawlowac60

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Scholar 22 months ago, created an answer that has been accepted. For A: Using E-Utilities/Entrez/Elink to access identical proteins

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