Questions tagged [refseq]

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Confusing naming in MANE GFF file

I'm working with the MANE v1.2 annotation (with RefSeq keys) and am puzzled about the ID naming convention being used. Specifically, there are several transcripts (18 by my count) that have hyphenated ...
merv's user avatar
  • 651
1 vote
1 answer

Is there a smaller representative version of refseq with fewer than 30K files in it?

Does any one have a condensed NCBI reference seq database with all the gbff files, which covers mostly all the bacteria and archaea. The current NCBI ReqSeq contains more than 30,000 gbff files. I am ...
flashton's user avatar
  • 217
1 vote
0 answers

Comparing common genes and transcripts between Gencode and Refseq

This is a very naive question - I am trying to compare and get the common lncRNA genes and transcripts between Gencode and Refseq from their gff files. Since their gene_id, gene_names are different, ...
beepboopbeep's user avatar
1 vote
1 answer

makeblastdb creating multiple files of unexpectedly large sizes

I have a set of 100 amino acid sequences and I want to perform a BLASTP sesrch against the refseq_protein database. Accordingly I had set up the standalone version ...
accibio's user avatar
  • 145
1 vote
2 answers

Understanding exercise on file coverage with question on summary statistics

I'm doing an exercise that asks for two files: Input 1: A target file (.bed format) contains multiple regions from ...
moth's user avatar
  • 111
-1 votes
1 answer

A database for RefSeq protein accession IDs

Are there any databases or tools that contain a list of all RefSeq protein IDs for the interest organism/microorganism, e.g. get a specific microorganism name and return all RefSeq Protein IDs that ...
Ehsan Salehabadi's user avatar
1 vote
1 answer

Mapping protein refseq to Gene ID

I have a protein refseq (eg, NP_000029). How can I get the corresponding gene ID (ag, APC) from NCBI using an R package?
Eliza Ganguly's user avatar
1 vote
0 answers

Filtering pileup from site lists

I want to write a script that filters a pileup file from a site lists file. As an input I get a reference genome, pileup and site lists files. Example of an output for this script: Pileup File : ...
Eliran Turgeman's user avatar
1 vote
0 answers

GCF VS GCA or combination of both for pangenomic studies

I have just started to learn bioinformatics and pangenomics. So if this question seems to you pretty basic then I apologize in advance. As we know, NCBI for the genome database, there are two kinds of ...
Furqan's user avatar
  • 87
0 votes
2 answers

Is it possible to obtain RefSeq transcripts from Ensembl database for GRCh37 to match Ensembl Genes?

I know that with GRCh38, it is possible to extract the matching RefSeq transcripts for Ensembl genes/transcripts/proteins using Biomart from Ensembl. However, for GRCh37, this option does not exists....
user324810's user avatar
  • 1,115
1 vote
1 answer

RefSeq transcript naming - transcript vs gene

I have a dataset composed on numerous RefSeq transcripts with names of the form NM_###### - essentially standard annotated mRNA accession numbers. I notice that numerous transcripts which have ...
KirkD-CO's user avatar
  • 175
1 vote
1 answer

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 ...
MrTomRod's user avatar
  • 191
4 votes
1 answer

blasting a refseq protein does not show the protein in the result set

Can anyone explain me, why I don't find a specific protein with a blast that was took before from the NCBI refseq database? Specifically, I was trying to blast the protein with the accession number "...
Matthias F.'s user avatar
5 votes
1 answer

Duplicate long hits from PSI-BLAST

I had a protein Refseq ID and I PSI-BLASTed this sequence against Refseq database. We all know that the Refseq is a Reference sequence database and it shouldn't have redundancy. After BLASTing my ...
Sara's user avatar
  • 777
7 votes
1 answer

Get RefSeq accession numbers with versions

Google searching for NM_002084 gives the following result: NM_002084.4 This, I assume, is the latest version v4, hence the .4 suffix. Searching for previous ...
zx8754's user avatar
  • 1,042
46 votes
5 answers

Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?

What are the actual differences between different annotation databases? My lab, for reasons still unknown to me, prefers Ensembl annotations (we're working with transcript/exon expression estimation)...
Plasma's user avatar
  • 563