Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • blastx against UniProt

    Is there any tool for doing alignment of local data against UniProt?

    For example,
    if i did an assembly for transcriptome , and i want to check the reliability of my contigs.
    How can i align it against UniProt or other Database?

    Thanks all

  • #2
    I think you answered your own question: use blast. A local copy of blast can be made to align your sequences against any local database that you have created via the use of 'formatdb'. As an example using the older blast (instead of blast+)

    'formatdb -i my_download_copy_of_uniprot -p T -n uniprot

    Then

    blastall -i my_local_sequences -d uniprot -p blastx -o out.blastx


    If you want a web-based solution then going to the source (http://www.uniprot.org/) will allow blasting.

    Comment


    • #3
      hi westerman,
      Did you mean that i have to download all the database?
      great idea!
      thanks

      Comment


      • #4
        Which of these is recommended for blast?
        UniProtKB/Swiss-Pro or UniRef100/90/50

        thanks

        Comment


        • #5
          Originally posted by papori View Post
          Which of these is recommended for blast?
          UniProtKB/Swiss-Pro or UniRef100/90/50

          thanks
          Well, it depends on what you are looking for. Thus you should be the one to decide after the descriptions of both. If I was to choose one for you I would go for UniRef because that will give you curated data without giving you false positives that you will need to chase down.

          Comment


          • #6
            Hi, you may try following sequence alignment web tool without installation/setup . Select Query Type - Nucleotide-Protein and search against database "SwissProt Protein UPKB"

            a. SynaBlast - single query submission - http://synasite.mgrc.com.my/synasuit...enu.jsp?modN=1
            b. SynaBlastMega - multiple query submission - http://synasite.mgrc.com.my/apps/syn..._BlastMega.jsp

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Exploring the Dynamics of the Tumor Microenvironment
              by seqadmin




              The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
              07-08-2024, 03:19 PM
            • seqadmin
              Exploring Human Diversity Through Large-Scale Omics
              by seqadmin


              In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
              06-25-2024, 06:43 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 07-10-2024, 07:30 AM
            0 responses
            24 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-03-2024, 09:45 AM
            0 responses
            201 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-03-2024, 08:54 AM
            0 responses
            210 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-02-2024, 03:00 PM
            0 responses
            192 views
            0 likes
            Last Post seqadmin  
            Working...
            X