Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • What does "non-redundant genomic sequence dataset" mean?

    Hello,

    I have read the paper "Identification of SNP and SSR markers in
    eggplant using RAD tag sequencing"

    Background The eggplant (Solanum melongena L.) genome is relatively unexplored, especially compared to those of the other major Solanaceae crops tomato and potato. In particular, no SNP markers are publicly available; on the other hand, over 1,000 SSR markers were developed and publicly available. We have combined the recently developed Restriction-site Associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of both SNP and SSR markers for eggplant. Results RAD tags were generated from the genomic DNA of a pair of eggplant mapping parents, and sequenced to produce ~17.5 Mb of sequences arrangeable into ~78,000 contigs. The resulting non-redundant genomic sequence dataset consisted of ~45,000 sequences, of which ~29% were putative coding sequences and ~70% were in common between the mapping parents. The shared sequences allowed the discovery of ~10,000 SNPs and nearly 1,000 indels, equivalent to a SNP frequency of 0.8 per Kb and an indel frequency of 0.07 per Kb. Over 2,000 of the SNPs are likely to be mappable via the Illumina GoldenGate assay. A subset of 384 SNPs was used to successfully fingerprint a panel of eggplant germplasm, producing a set of informative diversity data. The RAD sequences also included nearly 2,000 putative SSRs, and primer pairs were designed to amplify 1,155 loci. Conclusion The high throughput sequencing of the RAD tags allowed the discovery of a large number of DNA markers, which will prove useful for extending our current knowledge of the genome organization of eggplant, for assisting in marker-aided selection and for carrying out comparative genomic analyses within the Solanaceae family.


    and I don't understand the meaning of "non-redundant genomic
    sequence dataset" in abstract

    Could you help me, please?

    Thank you very much for your help

  • #2
    A non-redundant dataset is one where a single entry isn't repeated. For example, you are searching for something in a database and you find the same thing but in 2 different entries. That would mean there is redundancy within the dataset. A non-redundant database would be where there is only one entry

    Comment


    • #3
      do you know about "custom-made perl script" in RNA Seq analysis? is it a software?

      Comment


      • #4
        Originally posted by maryam p View Post
        do you know about "custom-made perl script" in RNA Seq analysis? is it a software?
        Not sure what reference this question is in but generally a perl script is a program written in Perl (a text processing programming language) for a specific purpose (custom part).

        Comment


        • #5
          Originally posted by maryam p View Post
          do you know about "custom-made perl script" in RNA Seq analysis? is it a software?
          That seems to be completely unrelated to this thread. In such situations, I suggest you create a new post rather than adding to an old and irrelevant thread.

          Comment


          • #6
            Thanks for your reply in a paper: https://www.ncbi.nlm.nih.gov/pmc/art...e.0129422.s001
            they have written:
            "GC counts of transcripts were determined using a custom-made perl script".
            I couldnt underestand diffinition of "custom-made perl script"
            many thanks

            Comment


            • #7
              "GC counts of transcripts were determined using a custom-made perl script".

              It means that indeed, they made a program that I guess takes each sequence, counst how many G and C's are and using a formula, calculates the percentage of GC in a whole sequence.

              Perl is a programming language.

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Techniques and Challenges in Conservation Genomics
                by seqadmin



                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                Avian Conservation
                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                03-08-2024, 10:41 AM
              • seqadmin
                The Impact of AI in Genomic Medicine
                by seqadmin



                Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                02-26-2024, 02:07 PM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 03-14-2024, 06:13 AM
              0 responses
              34 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-08-2024, 08:03 AM
              0 responses
              72 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-07-2024, 08:13 AM
              0 responses
              82 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-06-2024, 09:51 AM
              0 responses
              68 views
              0 likes
              Last Post seqadmin  
              Working...
              X