Questions tagged [ncbi]
Questions relating to information regarding, and use of resources from, the National Center for Biotechnology Information (NCBI). Please take care to ensure that questions are on-topic; see the help pages for more information.
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Creating a phylogenetic tree from my selected publicly-available sequences (WGS) in NCBI
I'm currently writing a paper on the comparison of virulence genes for a group of bacteria. I got my data from publicly-available whole genome sequences in NCBI. Now, I want to create a phylogenetic ...
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Why are there different gene expressions that are refered to the same gene in microarray experiments results?
I am studying gene expression profiling considering a dataset available on NCBI website. I do not understand the following: why are there some genes that have different profile and different ID ...
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How to download omic data from ncbi? (SRA data or any suggestion?)
I proposed myself to replicate the results in this paper with an accession number PRJNA325650. So, I'm trying to download the data. Which will be the best way to do this?. I tried with the sratoolkit, ...
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How to download different kinds of data from NCBI eutils?
I have been researching NCBI eutils and wish to get some 'big data' from it. I know that I can construct queries to query one of (I think) 8 databases, like this:
...
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From refseq ids to Go term Ids
I have a list of Refseq accession numbers such as :
YP_009448812
YP_009448725
YP_009448701
NP_659591
around 10 000 acc_numbers...
and I'm looking for a tools in ...
- 115
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How to recover all protein ses into refseq database
I'm actually trying to download all the virus protein sequences available in the NCBI database.
I guess the link is this one: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/
How could I get all ...
- 115
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Open Mass Spec Database
Wondering if there is an open (freely available) database of Mass Spec Data, particularly for the Substances/Compounds listed in NCBI.
Specifically, I am not sure if NCBI includes the mass ...
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Difference between NCBI's /genomes and /1000genomes
Wondering what the difference is in the data hosted here:
ftp://ftp-trace.ncbi.nih.gov/1000genomes
ftp://ftp.ncbi.nih.gov/genomes/
Also (sidenote), would be interested to note what the difference ...
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Taxonomy problems on algae: Is Cryptophyta a Phylum or a Class rank?
I am currently interested in algae taxonomy (I am not an expert in the field).
I retrieved the taxonomy of my sequences with their NCBI access number via the taxonkit software (https://bioinf....
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Why is GenBank growth slowing down?
https://www.ncbi.nlm.nih.gov/genbank/statistics/ shows the growth of the GenBank database is slowing since WGS (Whole Genome Shotgun) emerged. Is this happening because sequencing centers are ...
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What does "Origin" mean in NCBI GenBank?
I'm having trouble determining what exactly is meant by the term "Origin" in this case. It is just before a 70 bp sequence that the page claims is a plasmid, but does not specify it to be what I ...
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How to determine which is the nucleotide sequence of a gene?
I have came across a few genes that show different nucleotide sequence in different databases. I then found out that the sequences are actually reverse complement of each other. How do i determine ...
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Why was Achromobacter xerosis removed from the NCBI taxonomy?
The Global Catalogue of Microorganisms lists a bacterium called Achromobacter xerosis which is mentioned in several papers and patents. It once existed in the NCBI taxonomy database, with ID 216898. ...
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determining horizontal gene transfer between two genomes?
I want to determine if there is horizontal gene transfer between two genomes, in particular I was to use the parametric methods described in wikipedia since I would most likely struggle to understand ...
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moltype controlled vocabulary?
In submitting sequences using tbl2asn to NCBI/GenBank, the documentation states that there is a controlled vocabulary for the key "moltype", but no where on the Internet can I find a full list of that ...
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How to search NCBI in bulk for a list of accession numbers?
I have a large ( >100 ) list of accession numbers I want to look up and match to searches in NCBI (nucleotide); mainly for getting a tentative organism to match to the accession number.
ex:
...
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Finding phylogenetic distance between sequences?
I'm working on a piece of software that does comparative genomic analysis; and I found out in homology methods for functional annotation, it's preferable to pick the high scoring homolog from a ...
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Blast databases
I am helping a colleague setup a local blast server. My background is computer science so I apologize if I use incorrect terminology.
Using the NCBI blastn webpage, one of the databases listed is "...
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How do I download entire human genome for local blast formatting and searching?
I'm trying to make a copy of the entire human genome for local blast queries on my machine. I understand that I need to download it from the NCBI FTP server here...
ftp://ftp.ncbi.nih.gov/genomes/...
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146
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Finding protein motifs by running sequence analysis in protein BLAST
I've run the following sequence (bottom of page) in NCBI protein BLAST and its been identified as Zn-dependent alcohol dehydrogenase. Next I want to see what protein motifs are in this protein. Where ...
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How to conduct PSI-BLAST for a given protein sequence against bacterial protein database only?
I have a list of 100+ proteins and I need to conduct psi-blast for each one of them against "bacterial proteins" only.
I went to NCBI's protein blast tool, but couldn't figure out how to select/limit ...
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Where do I find standard tissue and cell names?
I am developing specialized database on some desease microarray experiments. The initial data is retreived from NCBI and ArrayExpress databases. The problem is that sample attributes sometimes specify ...
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Merge NCBI and Ensembl data
Apologies if this is a really naive question, but I cannot figure out how to do this easily. Here is a related post regarding the best method to find orthologous genes of a species.
Let's say I have ...
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Retrieve all predicted cds from NCBI
Please apologies if this has been answered somewhere else, but I couldn't find an answer to this problem.
I would like to retrieve all the predicted coding sequences on the NCBI ftp for a given ...
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How to get the correct RefSeq Protein transcript for a given RefSeq Nucleotide transcript?
How to get versioned Protein Accession Number for a Refseq Accession Number?
I have some versioned RefSeq Accession numbers and I would like to know their corresponding Protein Accession Numbers.
...
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How to search for a protein sequence of an specific taxa in NCBI?
My example: Sequence of HBB (Hemoglobin Beta) in Fishes.
How can I do a good search to obtain above sequences in NCBI? (I know hot to download them into a FASTA file)
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