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5 votes
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How to recover all protein ses into refseq database

As with most things, there are multiple ways to do this. Here are two of them: Download from the NCBI Assembly portal Go to https://www.ncbi.nlm.nih.gov/assembly/ and search for 'Viruses[Organism]'....
vkkodali's user avatar
  • 186
5 votes
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Difference between NCBI's /genomes and /1000genomes

The simplest difference is the scale and range. The aim of 1000 genome project was to provide comprehensive library of human genetic variation. DNA of individuals coming from different ethnic groups, ...
hibernicah's user avatar
3 votes
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Why is GenBank growth slowing down?

It is not really slowing down. The graph that you see in that link is semi-log. So the exponentiality of the growth has reduced. It is not surprising because we have much more data than what we had 10 ...
WYSIWYG's user avatar
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3 votes
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What does "Origin" mean in NCBI GenBank?

The ORIGIN may be left blank, may appear as "Unreported," or may give a local pointer to the sequence start, usually involving an experimentally determined restriction cleavage site or the ...
canadianer's user avatar
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3 votes

How to download different kinds of data from NCBI eutils?

Downloading all this using an E-utils search would be cumbersome as you would have to search against multiple databases. For your specific needs, a GTF/GFF3 file would be good. Basically, a GTF/GFF ...
WYSIWYG's user avatar
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3 votes
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Retrieve all predicted cds from NCBI

The GNOMON and GFF folder contains the files you want, the GNOMON if you check the README relates to the GNOMON gene predictor and the GFF I think links back to the same file. I think the file you ...
FoldedChromatin's user avatar
2 votes
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Why are there different gene expressions that are refered to the same gene in microarray experiments results?

What you are looking at there is a microarray dataset (see the description here). Microarrays are chips that have many sequence specific probes on them and sometimes they have multiple probes for the ...
Nicolai's user avatar
  • 4,391
2 votes

How to download omic data from ncbi? (SRA data or any suggestion?)

I had a look, I can see the data in FASTA format. The accession number is for a project with 50 samples, each of them a sequencing run. First I went to genbank at https://www.ncbi.nlm.nih.gov/ ...
Polypipe Wrangler's user avatar
2 votes

How to conduct PSI-BLAST for a given protein sequence against bacterial protein database only?

Your approach is correct but it is worth considering which database will work best for you. Questions to consider are; Does the database provide a large search space for the organism(s) you're ...
Michael_A's user avatar
  • 1,305
2 votes
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How do I download entire human genome for local blast formatting and searching?

You can either download and concatenate the individual chromosomes from NCBI or make your life easier and download a single fasta file from Gencode (note that that's the primary assembly, if you want ...
Devon Ryan's user avatar
2 votes

determining horizontal gene transfer between two genomes?

Since the parametric model is applied to only a single genome to see if there is evidence of recent HGT via a change in the average content in coding regions, it will not tell you from where the HGT ...
Tom V.'s user avatar
  • 321
1 vote
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From refseq ids to Go term Ids

So, I've looked a bit into this and the way you want to do your analysis won't work as you planned it. The main reason for this is that the GO database does not contain any virus species (as fas as I ...
Nicolai's user avatar
  • 4,391
1 vote
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Open Mass Spec Database

The Human metabolome database (HMDB) contains many MS/MS and NMR spectra for human metabolites. You can acquire the spectra from the downloads section. The HMDB includes external identifiers for each ...
Michael_A's user avatar
  • 1,305
1 vote

Difference between NCBI's /genomes and /1000genomes

In fact these two things are very different and I would say quite opposite. NCBI genomes are collection of information on genomes of various species including sequences, maps, chromosomes, assemblies,...
Maxim Kuleshov's user avatar
1 vote

Why was Achromobacter xerosis removed from the NCBI taxonomy?

For whatever it's worth, I queried NCBI support about this and got a reply: To: [email protected] Subject: Reason for removal of a species from the taxonomy? Hi, I notice that the ...
Mark Amery's user avatar
1 vote

moltype controlled vocabulary?

There is this "Controlled vocabulary for /mol_type qualifier" page created by the International Nucleotide Sequence Database Collaboration in 2013. It says the allowed values are: "genomic DNA", "...
mgkrebbs's user avatar
  • 9,054
1 vote

How to search NCBI in bulk for a list of accession numbers?

If you don't want to bother with BioPython, you can use Entrez Direct for this as follows: ...
vkkodali's user avatar
  • 186
1 vote

How to search NCBI in bulk for a list of accession numbers?

After some trial and error in an interactive python shell and some documentation checking, I found that the relevant information is present in the genbank-formatted output (...
bli's user avatar
  • 2,195
1 vote
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Finding phylogenetic distance between sequences?

No, because it is really not a binary decision. There are attempts to associate percent pairwise difference with taxonomic ranks (particularly species), but this is problematic because every ...
Karl Kjer's user avatar
  • 7,663
1 vote

Blast databases

With the blast binaries you get a perl script update_blastdb.pl which you can use to download preformatted databases from the ncbi (it's pretty much a script that ...
Carambakaracho's user avatar
1 vote

Finding protein motifs by running sequence analysis in protein BLAST

MOTIF search First of all this is not possbile in BLAST (at least nog direclty). There are a lot of tools to search for motifs in your sequence. I think a good way to start is to use MOTIF search. ...
KingBoomie's user avatar
  • 2,380
1 vote
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Where do I find standard tissue and cell names?

It turns out that ArrayExpress itself uses various ontologies (dictionaries structured as trees) available at Ontology Lookup Service when it processes users' search queries. Experimental Factor ...
Sashko Lykhenko's user avatar

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