Questions tagged [refseq]
The refseq tag has no usage guidance.
13
questions
1
vote
1
answer
123
views
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 ...
- 113
1
vote
2
answers
26
views
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
...
- 111
-2
votes
1
answer
46
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
vote
1
answer
31
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
vote
0
answers
32
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 :
...
- 133
1
vote
0
answers
129
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 ...
- 87
0
votes
2
answers
407
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....
- 960
1
vote
1
answer
94
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 ...
- 143
1
vote
1
answer
292
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 ...
- 191
4
votes
1
answer
27
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 "...
- 43
5
votes
1
answer
141
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 ...
- 757
7
votes
1
answer
373
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 ...
- 1,042
45
votes
5
answers
11k
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)...
- 553