User: Eli Korvigo

gravatar for Eli Korvigo
Eli Korvigo120
Reputation:
120
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Trusted
Location:
Russian Federation
Last seen:
2 days, 18 hours ago
Joined:
3 years ago
Email:
g********@me.com

Posts by Eli Korvigo

<prev • 18 results • page 1 of 2 • next >
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Merging alignments in ssu-align
... [ssu-align][1] is an HMM-based MSA tool for SSU sequences. It's bundled with three SSU models: archaeal, bacterial and eukaryotic. Given a set of archaeal and bacterial sequences the tool will first identify the best model for each sequence and produce two separate alignments for archaea and bacteri ...
alignment msa written 13 days ago by Eli Korvigo120
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Comment: C: Modifying fasta file based on vcf information
... Since the documentation is very scarce, it's hard to infer that `FastaVariant` ignores indels. You can see that in the [code](https://github.com/mdshw5/pyfaidx/blob/a088141d8c18d0420eb74a1ce1578c3c1ea7ef8f/pyfaidx/__init__.py#L1111). ...
written 9 weeks ago by Eli Korvigo120
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Comment: C: Modifying fasta file based on vcf information
... This might be an old question, but these days you can basically install any version of Java in a conda environment. Since your conda installation can be local, it will not require superuser rights. ...
written 9 weeks ago by Eli Korvigo120
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Comment: C: Phylogenetic Analysis Of Whole Genomes
... MrBayes is not an ML method. It's based on Bayesian inference. ...
written 4 months ago by Eli Korvigo120
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Comment: C: Phylogenetic Analysis Of Whole Genomes
... I wold recommend ssu-align for 16S multiple sequence alignment. It uses a 16S HMM. ...
written 4 months ago by Eli Korvigo120
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Answer: A: Phylogenetic Analysis Of Whole Genomes
... Genome-scale multiple sequence alignments are not quite good for phylogenies: they take a lot of time to compute and are never accurate. Moreover, it's hard to imagine a general-purpose sequence evolution model that would be equally adequate for protein-coding, rRNA, tRNA genes, repeats and other re ...
written 4 months ago by Eli Korvigo120
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Comment: C: Reference OTU-picking using pair-end reads without merging
... I literally lose > 99.9% of pairs even after a full-day worth of tuning trimming and joining parameters. ...
written 4 months ago by Eli Korvigo120
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Comment: C: Recommendations For Python Vcf Parser/Writer?
... CyVCF2 https://github.com/brentp/cyvcf2 ...
written 5 months ago by Eli Korvigo120
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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 13 months ago by Eli Korvigo120
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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 22 months ago by Eli Korvigo120

Latest awards to Eli Korvigo

Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
Appreciated 10 months ago, created a post with more than 5 votes. For A: Fetching Genbank Entries For List Of Accession Numbers.
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Fetching Genbank Entries For List Of Accession Numbers.
Supporter 22 months ago, voted at least 25 times.
Teacher 22 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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