User: Reece

gravatar for Reece
Reece250
Reputation:
250
Status:
Trusted
Location:
United States
Website:
http://linkedin.com/in...
Twitter:
reecehart
Last seen:
1 year, 10 months ago
Joined:
8 years, 10 months ago
Email:
r****@harts.net

Posts by Reece

<prev • 15 results • page 1 of 2 • next >
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Answer: A: Obtain Genomic Position From Codon # & Refseq
... Consider the Python hgvs package. [Disclosure: I'm one of the authors.] ...
written 3.4 years ago by Reece250
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Answer: A: How to get all the versions of refSeq
... Consider the Python hgvs package. [Disclosure: I'm one of the authors.] hgvs uses UTA, the Universal Transcript Archive, which is a collection of transcript versions from multiple sources with alignments to multiple references.   ...
written 3.4 years ago by Reece250
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Answer: A: Hgvs Nomenclature Lookup?
... Also consider the Python hgvs package. [Disclosure: I'm one of the authors.] You can synthesize python objects with ref and alt variants, and stringify them into hgvs. ...
written 3.4 years ago by Reece250
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Answer: A: Retrieve mutation position and ID for a mutation in hgvs format
... Also consider the Python hgvs package. [Disclosure: I'm one of the authors.] ...
written 3.4 years ago by Reece250
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Answer: A: hgvs name from variant information
... The hgvs python package has an experimental script to add a genomic HGVS tag to VCF files. See hgvs/misc/experimental/vcf-add-hgvs from the source package. You may extract that HGVS variant from the resulting VCF file and project it onto transcripts and protein sequences using the hgvs package, or m ...
written 3.4 years ago by Reece250
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Answer: A: Role of amino-acid change number
... It's also worth pointing out that a location in a sequence, including in the form above, is nearly useless when not associated with a sequence accession (e.g., NP_012345.6 or ENSP012345678). Not having an accession is like giving your address without a street name. Very many genes have multiple tran ...
written 3.4 years ago by Reece250
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Answer: A: python's HGVS module UTA connection error
... The OP also asked at the hgvs bitbucket page and the issue was solved there. The problem appears to be that the user's institution began blocking outgoing ports.     ...
written 3.4 years ago by Reece250
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Answer: A: How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
... Perhaps this Python solution will be useful to someone: from biomart import BiomartServer atts = ['external_gene_name','external_gene_source','ensembl_gene_id', 'ensembl_transcript_id','ensembl_peptide_id'] server = BiomartServer( "http://www.biomart.org/biomart" ) hge = server.datasets[ ...
written 3.9 years ago by Reece250
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Running splign just like NCBI
... NCBI exposes (e.g., via eutils) genomic coordinates for current transcripts on the current assembly only. I would like coordinates for older transcript versions on newer assemblies and for newer transcripts on older assemblies, and be reasonably confident that I'm mimicking NCBI behavior as closely ...
gnomon alignment splign written 3.9 years ago by Reece250
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Comment: C: Comprehensive Gene Sets
... Re: "UCSC re-aligns RefSeqs and these models differ from the original ones."... I investigated this pretty thoroughly last year. The two essential results are: 1) ~886 transcripts have *significant* genome coordinate discrepancies between RefSeq (splign) and UCSC (BLAT); and 2) When there's a discre ...
written 3.9 years ago by Reece250

Latest awards to Reece

Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Hgvs Nomenclature Lookup?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Hgvs Nomenclature Lookup?
Great Question 3.3 years ago, created a question with more than 5,000 views. For Recommendations For Python Vcf Parser/Writer?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How To Fetch A Gene By Exact Hgnc Gene Symbol With Eutils?
Appreciated 5.5 years ago, created a post with more than 5 votes. For Recommendations For Python Vcf Parser/Writer?
Good Question 5.5 years ago, asked a question that was upvoted at least 5 times. For Recommendations For Python Vcf Parser/Writer?
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Recommendations For Python Vcf Parser/Writer?
Student 5.5 years ago, asked a question with at least 3 up-votes. For Recommendations For Python Vcf Parser/Writer?

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