User: tdmurphy

gravatar for tdmurphy
tdmurphy190
Reputation:
190
Status:
Trusted
Location:
Last seen:
5 months, 1 week ago
Joined:
4 years, 3 months ago
Email:
t**********@gmail.com

Posts by tdmurphy

<prev • 23 results • page 1 of 3 • next >
0
votes
1
answer
202
views
1
answers
Comment: C: Why is asn2fasta so slow compared to efetch (when the sequence is not part of as
... I will second genomax's recommendation to contact NCBI's help desk. They'll at least be interested in what you're doing, and may have some suggestions on alternate approaches. Are you getting acceptable performance from annotwriter? It also has to do some remote lookups from NCBI servers, although ...
written 5 months ago by tdmurphy190
2
votes
1
answer
202
views
1
answers
Answer: A: Why is asn2fasta so slow compared to efetch (when the sequence is not part of as
... It probably has to do with efetch being able to resolve the sequence information locally on NCBI's servers, whereas asn2fasta is having to resolve each component sequence remotely. Not sure there's anything you can do about it. If you need large numbers of sequences from specific genomes, you'd be ...
written 5 months ago by tdmurphy190
0
votes
2
answers
651
views
2
answers
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 16 months ago by tdmurphy190
5
votes
1
answer
1.2k
views
1
answers
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 17 months ago by tdmurphy190
0
votes
2
answers
4.9k
views
2
answers
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 21 months ago by tdmurphy190
0
votes
2
answers
948
views
2
answers
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 23 months ago by tdmurphy190
2
votes
3
answers
1.9k
views
3
answers
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 23 months ago by tdmurphy190
1
vote
1
answer
1.2k
views
1
answers
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 2.2 years ago by tdmurphy190
0
votes
3
answers
1.2k
views
3
answers
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 2.2 years ago by tdmurphy190
0
votes
1
answer
948
views
1
answers
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 2.3 years ago by tdmurphy190

Latest awards to tdmurphy

Appreciated 16 months ago, created a post with more than 5 votes. For A: 'CDS' but not 'exon' in GFF
Scholar 16 months ago, created an answer that has been accepted. For A: Retrieve GFF3 file from ncbi
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: 'CDS' but not 'exon' in GFF
Scholar 2.3 years ago, created an answer that has been accepted. For A: Retrieve GFF3 file from ncbi

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1593 users visited in the last hour