User: Eli Korvigo

gravatar for Eli Korvigo
Eli Korvigo50
Reputation:
50
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Trusted
Location:
Russian Federation
Last seen:
1 week, 2 days ago
Joined:
2 years, 2 months ago
Email:
g********@me.com

Posts by Eli Korvigo

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Fetching Genbank Entries For List Of Accession Numbers.
... Yes, you need to change the `rettype` argument from `gb` to `fasta` ...
written 12 weeks ago by Eli Korvigo50
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Answer: A: extracting certain region 16sRNA from Silva
... I've recently developed a simple Python tool to extract 16S regions with respect to the reference E. coli notation (V4 is mapped from ~515 to ~810). The tool is openly available here https://github.com/grayfall/hypervar. You can install it using `pip`: `pip install git+https://github.com/grayfall/hy ...
written 9 months ago by Eli Korvigo50
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Comment: C: Fetching Genbank Entries For List Of Accession Numbers.
... Do you mean that the file has no sequence in it? There are some entries in GenBank that do not provide sequences, only annotation and metadata. If it's not the case, then I'll gladly help you and update the code. Waiting for your feedback. ...
written 11 months ago by Eli Korvigo50
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Answer: A: Fetching Genbank Entries For List Of Accession Numbers.
... Python 3 + BioPython with command-line interface. Basically, a less hardcoded and flexible version of Leszek's code, that doesn't fail when the list of accessions is so big, that GI retrieval results in `HTTP Error 414: Request-URI Too Large` #! /usr/bin/env python3 import argpar ...
written 16 months ago by Eli Korvigo50
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GenBank conflicting annotations (identical proteins with different exons)
... Here is the RefSeq mitochondrial complete genome record of Daucus carota DEFINITION Daucus carota subsp. sativus mitochondrion, complete genome. ACCESSION NC_017855 VERSION NC_017855.1 GI:386799229 DBLINK BioProject: PRJNA162951 It lists 2 identical proteins (NADH dehy ...
genome annotation refseq genbank written 16 months ago by Eli Korvigo50 • updated 16 months ago by Markus200
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Comment: C: Levenshtein Distance Vs Smith-Waterman Algorithm
... Yes, you are right.  ...
written 19 months ago by Eli Korvigo50
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Comment: C: Levenshtein Distance Vs Smith-Waterman Algorithm
... Levenstein distance is not a distance metric, hence you can't call it a "mathematical distance". ...
written 20 months ago by Eli Korvigo50
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Comment: C: Markov Chain For Generating Random Protein Sequences
... All links, but the last one, are dead. ...
written 23 months ago by Eli Korvigo50
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Comment: C: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
... In fact Ensembl's tool uses CrossMap http://www.ensembl.org/Homo_sapiens/Tools/AssemblyConverter?db=core ...
written 24 months ago by Eli Korvigo50
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Comment: C: Query UniProt for deleterious and neutral variations
... Thank you for your answer. The main point of the question is about sorting pathogenic variants, e.g. using the information from the "‘Pathology and Biotech" field.  ...
written 2.1 years ago by Eli Korvigo50

Latest awards to Eli Korvigo

Supporter 11 months ago, voted at least 25 times.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Fetching Genbank Entries For List Of Accession Numbers.

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