User: tdmurphy

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tdmurphy160
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Posts by tdmurphy

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Answer: A: How to download the feature table file of whole genome
... REDO sounds like it is specific for organelles -- is it valid to run on a whole genome? There are some annotated organelle sequences available for wheat, including two in RefSeq: https://www.ncbi.nlm.nih.gov/nuccore/?term=txid4565%5BOrganism%3Aexp%5D+AND+complete+genome%5Btitle%5D You can get featu ...
written 5 weeks ago by tdmurphy160
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Answer: A: 'CDS' but not 'exon' in GFF
... Organelles and prokaryote genomes in both GenBank and RefSeq are typically annotated with only CDS and no corresponding mRNA features, so the GFF3 has no exon features. This is mentioned briefly under "ANNOTATION DATA MODEL" in: ftp://ftp.ncbi.nlm.nih.gov/genomes/README_GFF3.txt ...
written 6 weeks ago by tdmurphy160
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Comment: C: What is the difference between GRCh37 and hs37? And hg19?
... > Ultimately GENCODE is the organization responsible for managing human/mouse genome data. They provide the authoritative genome data that is used by everyone including NCBI/UCSC/Ensembl. I believe you mean the [Genome Reference Consortium][1] manages the human and mouse genome data. GENCODE is ...
written 6 months ago by tdmurphy160
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Answer: A: How to download large protein data from NCBI?
... NCBI RefSeq includes nearly all bacteria proteins, and has files available for download at: https://ftp.ncbi.nlm.nih.gov/refseq/release/bacteria/ ...
written 7 months ago by tdmurphy160
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Answer: A: why the same gene is located at different chromosomes ?
... UCSC has two types of RefSeq tracks. The old "RefSeq Genes" or refgene track is based on alignments generated by UCSC, and can't distinguish between different locations with the same sequence. The newer "NCBI RefSeq" tracks are based on annotation imported from NCBI's RefSeq project, which uses addi ...
written 7 months ago by tdmurphy160
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Comment: C: Where I can download separate complete human chromosome genomes in GenBank forma
... [RefSeqGene][1] is a set of genomic records for individual clinically-relevant genes, not whole chromosomes. Genome annotation in GenBank flatfile format is available at: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.37_GRCh38.p11/GCF ...
written 11 months ago by tdmurphy160
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Answer: A: Easiest way to download all Enterobacteria
... You can easily do this from NCBI's Assembly resource: https://www.ncbi.nlm.nih.gov/assembly/?term=Enterobacteria%5Borgn%5D+latest_refseq%5Bfilter%5D click the blue "Download Assemblies" button, pick "refseq" and the filetype you're after (e.g. genomic FASTA), and it should work. It might take a whi ...
written 11 months ago by tdmurphy160
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Answer: A: Where to download gff3 file for EcoCyc data?
... I think EcoCyc uses the same IDs as EcoGene (EG#####), which are available on the GenBank and RefSeq annotations at NCBI. Try the "Download" links at the right from this page: https://www.ncbi.nlm.nih.gov/assembly/GCF_000005845.2 Both GFF3 and flatfiles are available. ...
written 11 months ago by tdmurphy160
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Answer: A: How to generate a new FASTA from an assembly-assembly mapping ?
... On the NCBI Remap FTP site, the alignment files for each assembly pair are provided twice (assm1/assm2 and assm2/assm1). The alignments themselves are flip-flopped for query and target, which would take care of most of your sorting problem. ...
written 11 months ago by tdmurphy160
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Answer: A: How to get Gene symbols & nuclotide FASTA for taxid :1239
... Many of the bacteria RefSeq genomes aren't available in NCBI's Gene database, so e-utils with the gene db won't work. If you have a specific set of assemblies in mind, try downloading the "feature_table.txt" files for that set and parsing what you need from there. e.g.: https://www.ncbi.nlm.nih.gov/ ...
written 11 months ago by tdmurphy160

Latest awards to tdmurphy

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: 'CDS' but not 'exon' in GFF
Scholar 12 months ago, created an answer that has been accepted. For A: Retrieve GFF3 file from ncbi

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