24
votes
Accepted
Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?
To add to rightskewed answer:
While it is true that:
Gencode is an additive set of annotation (the manual one done by Havana and an automated one done by Ensembl),
the annotation (GTF) files are quite ...
- 504
12
votes
Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?
Ensembl vs Gencode
https://www.gencodegenes.org/faq.html
The GENCODE annotation is made by merging the Havana manual gene annotation and the Ensembl automated gene annotation. [...] In practical ...
- 991
6
votes
Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?
To add practical advice to what others have said:
In a practical sense, I think the biggest difference between RefSeq and Ensembl/GENCODE is in the sensitivity/specificity trade off.
Ensembl aims ...
- 3,271
6
votes
Accepted
Get RefSeq accession numbers with versions
I don't believe this is possible using biomaRt, nor using AnnotationHub.
I have two suggestions, neither of them very ...
- 646
4
votes
Accepted
Is it possible to obtain RefSeq transcripts from Ensembl database for GRCh37 to match Ensembl Genes?
The RefSeq match option in BioMart is from the Matched Annotation from NCBI and EBI (MANE) collaboration between RefSeq and Ensembl. It has only been calculated for the up-to-date gene annotation on ...
- 1,749
4
votes
Accepted
RefSeq transcript naming - transcript vs gene
No, this is the same sequence. A single RefSeq accession will correspond to one sequence. However, nobody said that sequence needs to be unique in the genome. The specific sequence you are talking ...
- 9,452
2
votes
Mapping RefSeq-ID or NCBI-ID (Entrez-ID) to EC number
You can use Entrez Direct for this as follows:
efetch -db protein -id YP_805528.1 -format gpc -mode xml | xtract -insd Protein EC_number
YP_805528.1 6.3.2.13
- 1,266
2
votes
Accepted
blasting a refseq protein does not show the protein in the result set
NP_420767 is represented by the non-redundant refSeq protein WP_010919826, which has the same amino acid sequence. This is not very clearly annotated, but if you scroll down to the sequence in the ...
- 1,816
2
votes
Accepted
Duplicate long hits from PSI-BLAST
This is what is known as a feature, not a bug. Note that your identical proteins all have accessions starting with WP_. These are special "non-redundant ...
- 9,452
2
votes
Mapping protein refseq to Gene ID
You can do this with the reutils package, which provides an API to NCBI's E-utilities. Here's an example for your specific question:
...
2
votes
Accepted
makeblastdb creating multiple files of unexpectedly large sizes
Welcome to the Bioinformatics site! Hopefully you find the below helpful.
Regarding the creation of a RefSeq protein database locally...as you mentioned, there are pre-made RefSeq BLAST databases ...
- 782
1
vote
Is there a smaller representative version of refseq with fewer than 30K files in it?
proGenomes includes a collection of genomes that are representative of different types - https://progenomes.embl.de/download.cgi
Or Genome Updater could be used to filter on unique taxonomy IDs and ...
- 217
1
vote
Understanding exercise on file coverage with question on summary statistics
Based on the description in your question, I don't think this assumption is correct:
I believe what they refer in this exercise is that the target file should be something like the whole chr sizes of ...
- 9,452
1
vote
Is it possible to obtain RefSeq transcripts from Ensembl database for GRCh37 to match Ensembl Genes?
Try the GRCh37 version of BioMart, and the External reference "RefSeq mRNA ID" / "RefSeq ncRNA ID":
https://grch37.ensembl.org/biomart
From the Perl code provided by BioMart, it looks like the field ...
- 13.5k
1
vote
Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?
The UCSC Genome Browser Genes FAQ discusses this question in detail:
https://genome.ucsc.edu/FAQ/FAQgenes.html#ens
Officially, the Ensembl and GENCODE gene models are the same. On the
latest ...
- 111
1
vote
Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?
While annotations between RefSeq and Gencode are not so different is the coding regions (genes), Gencode is much more rich in the intergenic regions. This could be very advantagous for epigenetic ...
- 11
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