User: tdmurphy

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tdmurphy90
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Posts by tdmurphy

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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 3 months ago by tdmurphy90
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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 3 months ago by tdmurphy90
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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 3 months ago by tdmurphy90
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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 3 months ago by tdmurphy90
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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 3 months ago by tdmurphy90
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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 3 months ago by tdmurphy90
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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 3 months ago by tdmurphy90
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Answer: A: NameError: name 'utils' is not defined
... Have you tried NCBI's converter, to go straight from GFF3 to ASN.1 submission files? See: https://www.ncbi.nlm.nih.gov/genbank/genomes_gff/ ...
written 4 months ago by tdmurphy90
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Answer: A: NCBI map viewer fragile site are molecularly characterized or not.
... Those fragile sites correspond to a set of fragile site records defined by HGNC, and imported into NCBI Gene: https://www.ncbi.nlm.nih.gov/gene/?term=txid9606%5Borgn%5D+genetype_other%5Bprop%5D+fragile+site%5Bgene%2Fprotein+name%5D They're only defined by cytogenetic locations and aren't placed at ...
written 4 months ago by tdmurphy90
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Comment: C: Where can I download genomes of Retroviruses?
... From the NCBI retroviridae page, use the "retrieve sequences" menu in the upper right and select "RefSeq plus neighbor nucleotides", which will send you to this link: https://www.ncbi.nlm.nih.gov/nuccore?term=Retroviridae[Organism]+NOT+cellular+organisms[ORGN]+NOT+wgs[PROP]+NOT+AC_000001:AC_999999[p ...
written 4 months ago by tdmurphy90

Latest awards to tdmurphy

Scholar 4 months ago, created an answer that has been accepted. For A: Retrieve GFF3 file from ncbi

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