Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • BLAST+ strange results

    I am running command line blastn with a local copy of a microbial database. My command looks like

    blastn -query query.txt -db 16SMicrobial -out newres.txt -wordsize 11 -evalue 10 -gapextend 2 -gapopen 5 -penalty -3 -reward 1 This gives me 81 hits, they all have the same score such as

    Sequences producing significant alignments: Score (Bits) E Value

    ref|NR042397.1| Dokdonella fugitiva strain : A3 16S ribosomal R... 28.2 6.3
    ref|NR041093.1| Streptomyces rubiginosohelvolus strain NBRC 129... 28.2 6.3
    ref|NR041539.1| Kitasatospora kazusensis strain SK60 16S riboso... 28.2 6.3
    ref|NR041538.1| Kitasatospora saccharophila strain SK15 16S rib... 28.2 6.3
    ref|NR_044150.1| Streptomyces omiyaensis strain NRRL B-1587 16S ... 28.2 6.3
    ...

    Isn't that strange?

    Further, I repeated the query(same parameters) on the NCBI website, and that gave 162 hits. e.g.

    NC017551.1 Leptospira interrogans serovar Lai str. IPAV chromosome chromosome 1, complete sequence 398 398 100% 1e-108 100%
    NC008463.1 Pseudomonas aeruginosa UCBPP-PA14 chromosome, complete genome 398 398 100% 1e-108 100%
    NC_002516.2 Pseudomonas aeruginosa PAO1 chromosome, complete genome 398 398 100% 1e-108 100%

    I tried to compare the two, e.g. I looked for "Kitasatospora " from the former in the latter set of results, and could not find any matches. What am I doing wrong ?!

  • #2
    Originally posted by nupurgupta View Post
    I am running command line blastn with a local copy of a microbial database. My command looks like

    blastn -query query.txt -db 16SMicrobial -out newres.txt -wordsize 11 -evalue 10 -gapextend 2 -gapopen 5 -penalty -3 -reward 1 This gives me 81 hits, they all have the same score such as

    Sequences producing significant alignments: Score (Bits) E Value

    ref|NR042397.1| Dokdonella fugitiva strain : A3 16S ribosomal R... 28.2 6.3
    ref|NR041093.1| Streptomyces rubiginosohelvolus strain NBRC 129... 28.2 6.3
    ref|NR041539.1| Kitasatospora kazusensis strain SK60 16S riboso... 28.2 6.3
    ref|NR041538.1| Kitasatospora saccharophila strain SK15 16S rib... 28.2 6.3
    ref|NR_044150.1| Streptomyces omiyaensis strain NRRL B-1587 16S ... 28.2 6.3
    ...

    Isn't that strange?
    Not to me. Those scores are very poor and probably the worst that can be reported by BLAST for your database. So, although they are *hits* I doubt they are meaningful.

    Further, I repeated the query(same parameters) on the NCBI website, and that gave 162 hits. e.g.

    NC017551.1 Leptospira interrogans serovar Lai str. IPAV chromosome chromosome 1, complete sequence 398 398 100% 1e-108 100%
    NC008463.1 Pseudomonas aeruginosa UCBPP-PA14 chromosome, complete genome 398 398 100% 1e-108 100%
    NC_002516.2 Pseudomonas aeruginosa PAO1 chromosome, complete genome 398 398 100% 1e-108 100%

    I tried to compare the two, e.g. I looked for "Kitasatospora " from the former in the latter set of results, and could not find any matches. What am I doing wrong ?!
    I suspect your searching against different databases as the NCBI hits don't look like 16S matches to your queries.

    Comment


    • #3
      Thanks for the perspective. But I downloaded the microbial database from ncbi. ftp://ftp.ncbi.nlm.nih.gov/blast/db/16SMicrobial.tar.gz
      . I assumed that was the entire microbial database that online NCBI was also using for BLAST. Maybe not, let me see if I can find a FASTA file for all bacteria/microbes that I can use to build a database.
      Thanks very very much. This is a huge help

      Comment


      • #4
        It would help if you stated the name of the database you used on NCBI. Then a judgement can be made as to whether you're comparing like with like.

        Comment


        • #5
          I was using NCBI blast on microbial data.

          Comment


          • #6
            I am not surprised at all. My guess is that your query has a chance (and very short) match to a conserved sequence within the ribosomal 16s sequence. Have you tried looking at the alignments? I predict that every alignment will be the same.

            Comment


            • #7
              Yes, you are right! Sorry I am a newbie to this. Have found a bacterial database

              ftp://ftp.ncbi.nih.gov/gene/DATA/GEN...haea_Bacteria/

              Am going to get it now.

              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
              13 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 10-30-2024, 05:31 AM
              0 responses
              16 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
              52 views
              0 likes
              Last Post seqadmin  
              Working...
              X