Thanks for your second note, blancha. I didn't see it until after I posted my most recent note. I'll look at it more closely to see if it's better than what I came up with. It looks like it returns less irrelevant information in a single download, which is better.
Mark
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
So, I've found the answer, for those who may be interested. The file 'GCF_000001405.28_knownrefseq_alignments.gff3' (or the most recent version) in the directory 'ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/alignments/' maps every refSeq exon to the current human genome build. Plus you need the file 'gene2accession.gz' in 'ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/' to map the accession numbers to the geneIDs.
Thanks again.
Leave a comment:
-
Sorry, @memeri, I already deleted my last post, since I wasn't sure it answered your question. I'm putting the information back, since it probably does answer your question.
These are not one gene at a time methods.
You will get the entire annotation for the whole genome in one file.
You will have the location of each exon for all the genes.
The refSeq annotation of the exons can easily be downloaded from the UCSC Table Browser, using the RefSeq Track.
You can select the fields you want, if you don't want all the fields, as well as the format of the output file.
An alternative is to use Ensembl. You can just download a GTF file, or use biomaRt.
Here are the fields available in the refSeq track.
Code:name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames
I think that answers your question.
If it doesn't, I'll let someone else try.
And, I won't delete the post this time.
Leave a comment:
-
Thanks, blancha. These are, of course, browser based methods -- one gene at a time, butnice to know!
Leave a comment:
-
Thank you, mastal.
I was hoping for something a bit higher level than this, though. If I want to compile an up-to-date list of all annotated exons mapped to the current human reference genome assembly, I need to search through all 468 '...genomic.gbff' files in the 'vertebrate_mammalian' directory. In a somewhat random search of about 20 of these files, I didn't come across one with an entry from the current build (GRCh38.p2), and I don't see an index that may help me limit my search. I suspect that there may be a more direct route to this information; I'm sure NCBI does not search through all this every time they serve up a gene table.
Leave a comment:
-
-
refSeq gene tables -- all in one file?
Does NCBI have a single, downloadable file containing all refSeq-annotated exons for all genes? This information is available on a browser, one gene at a time, for example:
I'd like to maintain a local database with this information.
Latest Articles
Collapse
-
by seqadmin
Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...-
Channel: Articles
10-18-2024, 07:11 AM -
-
by seqadmin
Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.
Nobel Prize for MicroRNA Discovery
This week,...-
Channel: Articles
10-07-2024, 08:07 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 11-01-2024, 06:09 AM
|
0 responses
18 views
0 likes
|
Last Post
by seqadmin
11-01-2024, 06:09 AM
|
||
New Model Aims to Explain Polygenic Diseases by Connecting Genomic Mutations and Regulatory Networks
by seqadmin
Started by seqadmin, 10-30-2024, 05:31 AM
|
0 responses
18 views
0 likes
|
Last Post
by seqadmin
10-30-2024, 05:31 AM
|
||
Started by seqadmin, 10-24-2024, 06:58 AM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
10-24-2024, 06:58 AM
|
||
New AI Model Designs Synthetic DNA Switches for Targeted Gene Expression in Specific Cell Types
by seqadmin
Started by seqadmin, 10-23-2024, 08:43 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
10-23-2024, 08:43 AM
|
Leave a comment: