Questions tagged [refseq]

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1answer
43 views

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 ...
1
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1answer
26 views

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?
1
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0answers
28 views

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 : ...
1
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0answers
60 views

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 ...
0
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2answers
200 views

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....
1
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1answer
81 views

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 ...
1
vote
1answer
249 views

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 ...
4
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1answer
24 views

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 "...
5
votes
1answer
123 views

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 ...
7
votes
1answer
338 views

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 ...
45
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5answers
9k views

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)...