Stack Exchange Network

Stack Exchange network consists of 174 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.

Visit Stack Exchange

Questions tagged [ncbi]

The tag has no usage guidance.

2
votes
1answer
35 views

Importing GFF file with Biopython

Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file? For example, ...
0
votes
1answer
25 views

ncbi…eutils/esearch.fcgi: How to search now in the snp database?

According to the 2017(!) textbook, it worked at that time, for instance, https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=autism At ...
7
votes
1answer
88 views

ANY (technical) reason behind submitting sequences to GenBank versus ENA Sequence

The DNA sequence sections of the three INSDC databases (i.e., DDBJ, ENA Sequence and GenBank) are synchronized periodically and strive to keep their stored data as ubiquitously accessible as possible. ...
1
vote
1answer
13 views

Genomics: Downloading genomic data from the NCBI Genbank database

I'm taking a genomics course at school, and we have a final project due in a few weeks. Now, I can write bash scripts to sort and analyze the data, etc. However, I'm not quite sure how to actually ...
1
vote
1answer
32 views

Mapping RefSeq-ID or NCBI-ID (Entrez-ID) to EC number

I annotated my bacterial genomes using the new NCBI Prokaryotic Genome Annotation Pipeline and now, I want to annotate EC-numbers. In the master annotation file (.gff), I get the RefSeq-ID of every ...
2
votes
0answers
19 views

Does anyone have older versions of NT and 16s RNA DB from NCBI?

I am in search of past years' versions of NT and 16s databases from NCBI. I recently contacted NCBI about this and they replied: Unfortunately, we do not archive past versions of the blast ...
6
votes
1answer
52 views

Source for whole genome comparisons at NCBI Genomes

The NCBI Genomes database has these dendrograms for (presumably) whole genome comparisons for certain species, e.g. Pseudonomas aeruginosa or Escherichia coli. How were these comparisons done? ...
3
votes
1answer
104 views

How to automate NCBI genome download

I need to download all the completely assembled cyanobacterial genome's GenBank file(.gbff) from NCBI(RefSeq or INSDC ftp data). For this I think, the steps are: Need to find the completely ...
0
votes
1answer
24 views

Genebank Submission

I am not sure this kind of question is allowed here. I am asking because some of you might have already experienced this. I submitted some virus genomes in the Genebank. The genomes are on hold and ...
2
votes
2answers
64 views

Retrieving NCBI Taxa IDs from refseq or GenBank assembly accession

I have about 10,000 genome files all named by either refseq or genbank accession number, do you know if it's possible to convert these numbers to the corresponding NCBI taxon ID or species? for ...
2
votes
1answer
64 views

Download proteomes from NCBI based only on binomial names

I'm trying to download around 2000 proteomes from NCBI, but all I have is the genus and species e.g: lophodermium_seditiosum trichoderma_harzianum Does anyone know ...
1
vote
1answer
89 views

How to interpret a PSSM matrix from PSI-Blast - what do the numbers represent?

PSI-Blast on a sequence returns a PSSM matrix file containing two matrices, one to the left, one the the right, for all amino acids: ...
4
votes
1answer
79 views

What does an output of -I for all amino acids mean in a psi-blast pssm matrix file?

I have run psi-blast using the NR database, remotely, with one iteration, for several sequences to calculate an evolutionary profile (PSSM) for each of those sequences. However, many of the PSSM ...
0
votes
1answer
27 views

NCBI xml-format Printing nodeValues from tags with the same names

I would like to retrieve all Other-source_anchor on the level of DNA binding from within a Gene Ontology XML file using php. If I try this with my code, I only get Gene Ontology back and not the ...
0
votes
3answers
70 views

Generating multiple NCBI URLs with eutils

I would like to create a URL that takes input from different arrays to generate a search. The data I would like to retrieve is from NCBI. Below you can find the code I wrote. But I can't get it to ...