Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

  • #2
    See the ftp downloads site:

    ftp://ftp.ncbi.nlm.nih.gov/refseq/release/

    Comment


    • #3
      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.

      Comment


      • #4
        Thanks, blancha. These are, of course, browser based methods -- one gene at a time, butnice to know!

        Comment


        • #5
          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
          You may have to work a bit to get exactly the format you want, but all the information is available from the UCSC Table Browser, Ensembl, and probable GenCode.

          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.

          Comment


          • #6
            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.

            Comment


            • #7
              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

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Choosing Between NGS and qPCR
                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,...
                10-18-2024, 07:11 AM
              • seqadmin
                Non-Coding RNA Research and Technologies
                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,...
                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 seqadmin  
              Started by seqadmin, 10-30-2024, 05:31 AM
              0 responses
              18 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 10-24-2024, 06:58 AM
              0 responses
              24 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 10-23-2024, 08:43 AM
              0 responses
              53 views
              0 likes
              Last Post seqadmin  
              Working...
              X