User: tdmurphy

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tdmurphy110
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Posts by tdmurphy

<prev • 19 results • page 1 of 2 • next >
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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 4 months ago by tdmurphy110
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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 5 months ago by tdmurphy110
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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 5 months ago by tdmurphy110
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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 9 months ago by tdmurphy110
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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 9 months ago by tdmurphy110
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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 9 months ago by tdmurphy110
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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 9 months ago by tdmurphy110
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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 9 months ago by tdmurphy110
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Answer: A: Human chrY analysis
... The files in the CHR_* directories are for the scaffolds assigned to each chromosome, including the set of 13 scaffolds used to make the GRCh38 Y chromosome plus 3 extra unlocalized scaffolds assigned to chrY but not yet incorporated into the chromosome. If you want the assembled chrY sequence, try ...
written 9 months ago by tdmurphy110
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Answer: A: Get all completely sequenced genomes from one genus
... This is easily accomplished from NCBI's Assembly resource: https://www.ncbi.nlm.nih.gov/assembly/?term=bacteria%5Borgn%5D+latest_refseq%5Bfilter%5D+complete_genome%5Bfilter%5D You can download FASTA, annotation, or other files using the big blue "Download Assemblies" button. Note "complete genome" ...
written 9 months ago by tdmurphy110

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Scholar 10 months ago, created an answer that has been accepted. For A: Retrieve GFF3 file from ncbi

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