User: Eli Korvigo

gravatar for Eli Korvigo
Eli Korvigo80
Reputation:
80
Status:
Trusted
Location:
Russian Federation
Last seen:
21 hours ago
Joined:
2 years, 4 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 4 months ago by Eli Korvigo80
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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 11 months ago by Eli Korvigo80
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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 13 months ago by Eli Korvigo80
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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 18 months ago by Eli Korvigo80
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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 18 months ago by Eli Korvigo80 • updated 18 months ago by Markus200
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Comment: C: Levenshtein Distance Vs Smith-Waterman Algorithm
... Yes, you are right.  ...
written 21 months ago by Eli Korvigo80
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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 22 months ago by Eli Korvigo80
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Comment: C: Markov Chain For Generating Random Protein Sequences
... All links, but the last one, are dead. ...
written 2.1 years ago by Eli Korvigo80
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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 2.1 years ago by Eli Korvigo80
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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 2.2 years ago by Eli Korvigo80

Latest awards to Eli Korvigo

Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Fetching Genbank Entries For List Of Accession Numbers.
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Fetching Genbank Entries For List Of Accession Numbers.
Supporter 13 months ago, voted at least 25 times.
Teacher 13 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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