Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • download all gene sequences

    hi

    I want to download all known human gene sequences available till date. Is there a way to get it? I got the list of genes from UCSC ( http://genome.ucsc.edu/knownGeneLists.html ). But how do I download the gene sequences for all of them??? Please suggest...

    thanx
    sina

  • #2
    Go to the UCSC Table browser: http://genome.ucsc.edu/cgi-bin/hgTables?command=start
    Group: genes and gene prediction tracks.
    Output format: sequence.
    cheers,
    s.

    Comment


    • #3
      hi steven

      thanx for your immediate reply....i was out of station, so couldnt reply soon.....
      i had looked at the table browser option before....but in the results the gene name is not available...instead they give the code of the gene name assigned by uscs for each gene (which is mentioned in the link i posted before in this thread).....
      what i require is the sequences of all the genes with the headers being their names....i also want the exons, introns, etc differentiated in the same sequence....since these are available in the database there should be an option of retrieving them easily....can u pls suggest a way....

      thanx
      sina

      Comment


      • #4
        1. Go to the UCSC Table browser: http://genome.ucsc.edu/cgi-bin/hgTables?command=start
        Try it, this has nothing to do with the link you mentioned.
        Select the options as shown in the attached screenshot (this is an example, you may prefer another reference annotation like UCSC or Ensembl, but make sure the assembly version is the one you need).

        2. On the next screen, select "genomic" (i believe you want transcription units, not mRNA sequences) and click on "submit".

        3. On the next screen you will find a wonderful interface that proposes you all the options you can dream of regarding how to retrieve your sequence (include upstream/downstream flanks, what to display in upper/lower case, etc).

        Enjoy,
        s.
        Attached Files

        Comment


        • #5
          thank you very much

          steven,
          thanks for the tip--I do not know if I am oil or water but I am planning to explore Galaxy

          Comment


          • #6
            i got it...thanks a lot steven!!!

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Essential Discoveries and Tools in Epitranscriptomics
              by seqadmin


              The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
              Yesterday, 07:01 AM
            • seqadmin
              Current Approaches to Protein Sequencing
              by seqadmin


              Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
              04-04-2024, 04:25 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 04-11-2024, 12:08 PM
            0 responses
            55 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 10:19 PM
            0 responses
            51 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 09:21 AM
            0 responses
            45 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-04-2024, 09:00 AM
            0 responses
            55 views
            0 likes
            Last Post seqadmin  
            Working...
            X