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10
votes
3
answers
1.8k
views
9 follow
3
answers
efetch error LWP::Protocol::https not installed
efetch written 16 months ago by traviata • 10 • updated 14 days ago by Liam Thompson • 120
0
votes
2
answers
746
views
2
answers
web efetch Json out put which is not a real json
python efetch json biopython pubmed written 17 months ago by Lilizine • 0 • updated 22 days ago by MatthewP • 60
1
vote
1
answer
167
views
1
answer
Different output fields from efetch
python efetch sequence written 11 weeks ago by Medhat ♦ 8.2k • updated 11 weeks ago by Pierre Lindenbaum ♦ 117k
2
votes
3
answers
2.3k
views
3
answers
Entrez direct E-utilities - "efetch" command to retrieve CDS with protein accessions does not work
entrez direct e-utilities cds efetch retrieve written 2.4 years ago by al-ash • 100 • updated 4 months ago by h.mon ♦ 23k
0
votes
1
answer
182
views
1
answer
Which tool to use to get all citations of a pmid paper?
entrez eutils efetch written 4 months ago by Saad Khan • 310 • updated 4 months ago by h.mon ♦ 23k
2
votes
1
answer
215
views
1
answer
Strand not working in biopython efetch
efetch biopython strand written 5 months ago by tim.ivanov.92 • 10 • updated 5 months ago by jrj.healey ♦ 10k
2
votes
1
answer
457
views
1
answer
Getting taxid from accession number
taxid efetch taxonomy genbank eutils written 10 months ago by auninsaw • 10
7
votes
3
answers
1.2k
views
3
answers
Retrieve GFF3 file from ncbi
gff3 ncbi efetch written 12 months ago by john • 70 • updated 10 months ago by ucpete • 20
5
votes
3
answers
526
views
3
answers
Cannot get efetch to download genome - what is wrong?
genome fasta efetch entrez written 10 months ago by BioBing • 100 • updated 10 months ago by h.mon ♦ 23k
0
votes
1
answer
415
views
1
answer
To get the name of the strains by searching assembly genome number GCF_
ncbi python efetch written 13 months ago by horsedog • 30 • updated 13 months ago by Joseph Hughes • 2.7k
0
votes
1
answer
874
views
5 follow
1
answer
Fetching NCBI gene symbols from NCBI protein ids or GI identifiers
ncbi gene efetch entrez written 15 months ago by Vijay Lakhujani ♦ 3.6k • updated 15 months ago by Puli Chandramouli Reddy • 150
6
votes
1
answer
837
views
1
answer
How to download all sequences of a list of proteins for a particular organism
entrez direct efetch esearch written 16 months ago by traviata • 10 • updated 16 months ago by Kevin Blighe ♦ 37k
0
votes
1
answer
472
views
1
answer
Nested loops write in xml
python loop biopython efetch xml written 17 months ago by Lilizine • 0
1
vote
1
answer
787
views
1
answer
NCBI Entrez - efetch from PMC returns only abstract
efetch entrez pmc written 18 months ago by chaniart • 0 • updated 18 months ago by Jean-Karim Heriche ♦ 18k
10
votes
1
answer
2.1k
views
11 follow
1
answer
Download NCBI genomes using taxonomy id (taxid)
ncbi python efetch biopython written 23 months ago by David • 140 • updated 18 months ago by pedrorodrigues • 10
1
vote
0
answers
814
views
0
answers
Entrez progammaticly: Direct efetch or epost + efetch
epost efetch entrez written 18 months ago by guedes.aureliano • 0
0
votes
1
answer
855
views
1
answer
URL for NCBI Efetch + XML with full annotation table
ncbi xml efetch eutils annotation written 20 months ago by Pierre Lindenbaum ♦ 117k • updated 20 months ago by genomax ♦ 62k
2
votes
1
answer
617
views
1
answer
Mistakes in a bash script for adding taxid for nt database
taxid efetch nt database shell bash written 20 months ago by wyc661217 • 10 • updated 20 months ago by Istvan Albert ♦♦ 79k
0
votes
1
answer
827
views
1
answer
Transfer GI to taxID by efetch in a loop
software error taxid efetch gi written 21 months ago by wyc661217 • 10
0
votes
1
answer
890
views
1
answer
Using efetch(biopython) to get the fasta file of an mRNA, as well as the exon locations
python efetch biopython entrez written 21 months ago by Jacob • 10 • updated 21 months ago by Ben • 50
7
votes
1
answer
660
views
1
answer
Extract Bibliographic Reference from GEO dataset using EFetch?
geo ncbi efetch written 21 months ago by Tom • 20 • updated 21 months ago by Santosh Anand ♦ 4.6k
3
votes
2
answers
3.1k
views
2
answers
Difference between NCBI Entrez formats (e.g., xml, docsum) for efetch
ncbi edirect efetch entrez command-line written 4.8 years ago by paulparsons • 130 • updated 22 months ago by DCGenomics • 310
0
votes
0
answers
721
views
0
answers
Getting DNA sequences by ncbi eutils for a specific assembly e.g.: hg19, hg38, GRCh37.p13 or GRCh38.p6?
ncbi eutils efetch dna sequences written 2.2 years ago by burcakotlu • 40
4
votes
2
answers
1.5k
views
2
answers
How can we download all TSA and WGS from NCBI Trace by taxon programmatically?
ncbi assembly trace efetch eutils written 2.3 years ago by Michael Dondrup ♦ 45k
0
votes
2
answers
1.4k
views
2
answers
How to retrieve any and all NCBI/GenBank accession numbers from a Taxonomy ID?
ncbi accession number efetch taxid bioinformatics written 2.3 years ago by yarmda • 0
0
votes
1
answer
678
views
1
answer
How to pass multiple seq_start and seq_stop statements to NCBI efetch
ncbi efetch sequence entrez written 2.4 years ago by massa.kassa.sc3na • 0
1
vote
1
answer
1.9k
views
1
answer
How to get correct Taxonomy UID from NCBI Taxonomy using Entrez E-utilities efetch?
ncbi efetch entrez biopython e-utilities written 2.6 years ago by JV • 380 • updated 2.6 years ago by piet • 1.6k
4
votes
1
answer
1.1k
views
1
answer
NCBI feature table sequence extraction
ncbi efetch programming written 2.7 years ago by Prasad • 1.5k • updated 2.7 years ago by Sej Modha ♦ 4.0k
1
vote
1
answer
1.0k
views
1
answer
Fetching multiple FASTA from NCBI
ncbi efetch written 2.7 years ago by mikael.lenz.strube • 40 • updated 2.7 years ago by piet • 1.6k
1
vote
0
answers
1.4k
views
0
answers
Find an existing nucleotide sequence for a specific protein sequence through NCBI eutils
efetch sequence esearch elink eutils written 3.2 years ago by Jenez • 510
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