Questions tagged [ncbi]

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4 votes
1 answer
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How to promote assemblies into genomes in NCBI?

Note: I've never submitted an assembly/genome to NCBI, so excuse if my perspective is flawed. I'm working with Drosophila subobscura. (spring fruit fly) I see here https://www.ncbi.nlm.nih.gov/data-...
3 votes
0 answers
28 views

How are BLAST record scores calculated in biopython

Can someone explain how the score is calculated for Bio.Blast.Record.Description? For example, if Record.Description.num_alignments is >1, is ...
2 votes
0 answers
26 views

Why does segmasker modify headers?

When parsing NCBI BLAST+ segmasker output, I realized the program modifies almost every header containing these strings: ( or )...
  • 185
2 votes
0 answers
492 views

Cannot blast against specific NCBI databases

I am having issues with some prokaryote reference genome databases (exact names : ref_prok_rep_genomes.*), that I downloaded from the NCBI website : https://ftp.ncbi.nlm.nih.gov/blast/db/. Files in ...
2 votes
0 answers
39 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 ...
  • 245
1 vote
0 answers
19 views

segmasker doubles found intervals

During NCBI BLAST+ segmasker output exploration, I found out that for some sequences, the program returns the same interval twice: ...
  • 185
1 vote
1 answer
21 views

Retrieval protein definition from accession ID

I have a list of protein accessions: XP_025107904.1 PVD22034.1 AJA37836.1 How can I obtain the definition of the protein, and the related organism? Output: ...
  • 131
1 vote
1 answer
45 views

Getting translation table of organisms through Entrez direct (or other CLIs)

I have a long list of NCBI taxonomic ids for organisms and I want to write a script to get their corresponding translation tables. Is there a way to do this through Entrez? (packages in R, Python etc. ...
1 vote
0 answers
52 views

Downloading exon-wise gene sequence using commandline

I want to download exon-wise gene sequence of around 200 genes from NCBI. Is there anyway to do this from terminal? I have the transcript id for each sequence and I am using efetch command to download ...
1 vote
0 answers
30 views

Tool that can sort NCBI taxonomy ids based on phylogeny

I have a set of NCBI txids (of varying ranks) that I want to sort in some way (e.g. a table or a tree, the way it is sorted isn't super important), based on the current NCBI data for phylogenetic ...
  • 11
1 vote
0 answers
18 views

How to interpret complete genome sequence in NCBI

I have a very basic and quick question: does the complete sequence of nucleotides of an organism (for example this one that I am considering in my homework of Pyrococcus Fuoriosus) reported in NCBI ...
1 vote
0 answers
132 views

How to read E-value annotation on NCBI BLAST?

I am seeking clarification on how to read the E value annotation on NCBI's BLAST results. What I understand so far: E -values are the expected value of the number ...
1 vote
0 answers
65 views

How to deal with the mismatches between gene names obtained from different sources?

For most of the time, I rely on gene ids to combine different datasets. However, in some instances, I have to combine datasets based on gene names. Then, if I don't know the source of gene names in ...
1 vote
0 answers
27 views

Generating taxonomic hierarchy by species/genus name

I am attempting to create a reference library of DNA plant barcodes in the ITS2 barcode region for plants from a specific region (Panama). I downloaded all the sequences for plants that resulted in a ...
  • 21
1 vote
0 answers
21 views

mining DNA barcodes from Genebank/BOLD per location

Is there a method to download all the sequences for a particular geographic region (Panama) for 'DNA barcode' sequences (ITS2, rbcL or trnL). Hopefully, the specimen collection location will include ...
  • 21
1 vote
0 answers
60 views

How to (efficiently) search nuccore to retrieve only annotated sequences?

I wish to efficiently search nuccore to retrieve only annotated sequences. By "annotated" I mean that the nuccore entry contains annotation information. An equivalent definition (if I understand ...
1 vote
0 answers
45 views

Is there a built-in parser for the textual feature table that Entrez.efetch returns?

Entrez.efetch helpfully gives me the feature table of a nuccore entry. If I understand correctly, efetch can only return the ...
1 vote
1 answer
70 views

How can extract the list of genes name from the raw data in GEO?

The format of the raw data that upload in GEO is different, like TXT, CEL or other form. How can I extract the list of genes name from these formats? And then how can I normalize them with R? I would ...
0 votes
1 answer
49 views

How can I get data of single cell RNA sequence with raw count?

I am using dataset GSE85241, but I can't find the read counts of the dataset. It only provides with RPKM values. How can I find the read counts of a dataset?
0 votes
0 answers
94 views

How to download metadata in SRA (i.e., SraRunTable.txt) using Unix commands?

We can obtain metadata (the SraRunTable.txt file) from the webpages in SRA. How to get this file using Unix commands? A potential solution was given in https://bioinformatics.stackexchange.com/a/...
  • 113
0 votes
0 answers
12 views

xtract from eutilities not exctracting the information I need

I'm running the following command which uses the NCBI e-utilities: esearch -db bioproject -query "PRJNA198476 [PRJA]" | esummary This returns: ...
0 votes
1 answer
23 views

How do you search for new enzymes that are more stable for handling, immobilization?

Noob here. I get that I should deduce what characteristics the ideal new enzyme should meet, and then use tools such as PDB and blast to compare to the old enzymes, and use other tools such as pymol, ...
0 votes
0 answers
29 views

How do I generate a list of post-synaptic gene markers that will guide me in my search for these markers in intestinal stem cells?

I would like to generate a list of gene markers that represent post-synaptic related genes. I will then use this list to search through single cell sequencing data, in order to assess whether certain ...