User: ostrokach

gravatar for ostrokach
ostrokach280
Reputation:
280
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Trusted
Location:
Canada
Last seen:
2 months, 1 week ago
Joined:
4 years, 9 months ago
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Posts by ostrokach

<prev • 20 results • page 1 of 2 • next >
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Set up a blast remote server
... I know that `blastp` has a `-remote` option, which allows you to run your query on NCBI servers (see [here](https://www.ncbi.nlm.nih.gov/books/NBK279680/)). Is there a way I can set up my own remote server that could be queried using `blastp` and would run queries against my own custom database? I ...
blast written 18 months ago by ostrokach280 • updated 18 months ago by st.ph.n2.4k
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Answer: A: VCF to Uniprot Mutation
... The best tool that I could find for annotating VCF files with UniProt mutations is [Oncotator](http://portals.broadinstitute.org/oncotator/). It explicitly provides "Site-specific protein annotations from UniProt". Alternatively, you can annotate VCF files with *Ensembl* mutations, and then map Ens ...
written 2.6 years ago by ostrokach280
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Comment: C: Align human reference genome and ancestral genome
... Thanks very much for your input! I was following the methods for [CADD](http://cadd.gs.washington.edu/), but I guess they had to do the alignments at the genome level in order to be able to analyse non-coding variants. I looked at your ensembl link, but could not find any pairwise alignments that I ...
written 2.6 years ago by ostrokach280
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Align human reference genome and ancestral genome
... I would like to get a list of amino acid mutations that occured in the course of evolution from early primates to current humans. I found the `homo_sapiens_ancestor_GRCh38_e86.tar.gz` file on the Ensembl ftp site (ftp://ftp.ensembl.org/pub/release-86/fasta/ancestral_alleles/), which, as I understan ...
genome alignment written 2.6 years ago by ostrokach280 • updated 2.6 years ago by Jean-Karim Heriche18k
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Comment: C: VCF to Uniprot Mutation
... The reason I called VEP a black box is because it isn't clear where the data comes from (this is my gripe with Biomart as well). It is easy to see the Uniprot checkbox and feel that it does what you want it to do. But then several steps down your pipeline you realise that 30% of your mutations don' ...
written 2.9 years ago by ostrokach280
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Comment: C: VCF to Uniprot Mutation
... I am hesitant to use VEP (or other web services) because to me they are black boxes (I am not a Perl expert) and they do not scale to millions of mutations. As far as I understand, VEP relies on the Ensembl Core and Variation databases. However, those databases map to UniProt through gene identifier ...
written 2.9 years ago by ostrokach280
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Comment: C: VCF to Uniprot Mutation
... Thank you for your answer! As you point out, Ensembl and consequently UniProt only have access to COSMIC v71. One of the things I am trying to accomplish is to map variants in a more recent version of COSMIC to UniProt. ...
written 2.9 years ago by ostrokach280
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VCF to Uniprot Mutation
... Does anyone know of a tool for converting SNPs in VCF format to amino acid mutations in UniProt proteins? ---- I know `snpEff` can do this for Ensembl variants. For example, for the VCF file with the line: 1 69538 COSM75742 G A . . `snpEff` adds the following annotation: 1 69538 COS ...
snpeff uniprot snp written 2.9 years ago by ostrokach280
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Answer: A: Where can I look for highly-reliable experimentally-validated PPI interactions?
... [Mentha][1] integrates PPI data from different resources, assigning a score to each interaction and providing a mapping to UniProt IDs. [1]: http://mentha.uniroma2.it/about.php ...
written 3.0 years ago by ostrokach280
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Comment: C: Workflow management software for pipeline development in NGS
... Nothing really... just thought I'd point it out. I spent a bit of time looking through the nextflow website before realizing that it's written in groovy. Most of the code I run is written in C / C++ / Python, so I would rather use a workflow manager written in one of those languages. It makes it e ...
written 3.0 years ago by ostrokach280

Latest awards to ostrokach

Popular Question 14 months ago, created a question with more than 1,000 views. For VCF to Uniprot Mutation
Popular Question 18 months ago, created a question with more than 1,000 views. For HGMD mutation naming convention
Student 2.6 years ago, asked a question with at least 3 up-votes. For VCF to Uniprot Mutation
Scholar 2.6 years ago, created an answer that has been accepted. For A: VCF to Uniprot Mutation
Pundit 2.8 years ago, created a comment with more than 10 votes. For C: Blast - Formatting Output
Voter 3.0 years ago, voted more than 100 times.
Appreciated 3.5 years ago, created a post with more than 5 votes. For C: Blast - Formatting Output
Commentator 3.7 years ago, created a comment with at least 3 up-votes. For C: Blast - Formatting Output
Supporter 3.8 years ago, voted at least 25 times.

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