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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.

26 questions
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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 the phylogenetic methods fully. The two genomes…
Ro Siv
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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 species. Let's say my interest species today is…
tlorin
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3
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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 between ftp-trace and just ftp is. But there is…
Lance
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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 submitting their data unannotated (WGS submissions are…
player87
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3
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1 answer

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. According to the RefSeqFAQ …
ChrisGuest
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2
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1 answer

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.shenwei.me/taxonkit/usage/). I noticed that I get…
Tof
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2
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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 assume is incomplete, seeing as I don't think there is…
CDB
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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: KJ841938.1 would match to Setoptus…
Ro Siv
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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 tree for these species but since I'm working from…
rimuru
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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:…
Joey Gough
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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 R or Python in order to get the corresponding Go term ids. I tried the packages…
Grendel
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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 spectrometry data / datafiles in their FTP server related to…
Lance
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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. However, it is no longer there - going to…
Mark Amery
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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 vocabulary. "mRNA" and "genomic" are given as…
David Maddison
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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 "NCBI Genomes (chromosome)." I'm unable to find this…
cbake
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