Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • garethboy
    Member
    • Feb 2012
    • 19
    #1

    How to do annotation after gene prediction?

    Dear all,

    I am pretty new in bioinformatics. I want to ask, after I perform gene prediction using PRODIGAL, I got the following:


    PHP Code:
    >final_001_R1_00001 # 2 # 898 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.644
    ATGCCAGCAGGTCGATTGGCCAAGCCACTGGAGGCAATCGCGGGCCCGCTGCGGCGGTCA
    TCGCCGGAGTCCGTTGACCGGATGCTCATCGGCTTGTGCGCGGTCATCTGGTTGGCGTTC
    GTCGGGATGCTGGTCGGTGCCATCGTGGTGATCGCCGGAATGGGGGAGGACTCGGGTTCG
    TCGGGGTCTTCGTGGGGCATCTACATCGTCATCGGGGTATCGCTGGCCGTCATCGTCGGT
    GCCGTGCCGCTGTTGCTACGTGCCCGCAACACCGCTGCCCAGCGCACCTCGAAAACGGCC
    CCTAAAACCAAGGGCGCCAATTCCTCCGGTGGGGCCACTGCGCCGTCTGGACCGCCTCCC
    GCGGAGGCGTCGACCGAGAAGCTCAAGACCTTCGGTGGTCTCGCCGATCACGTGAGCCAT
    GTTCCCAAGGACTACAACGGTCCTGGGTCACCCGCGTACCGGGCAGCCACCGAGGCGGCC
    GCGAAGAGGGCGGTGGTCAACCGGCTGTGGTTGCGGGCCACGGTGGGGATCGCCGGCGCG
    ATCGGCCTGGCACTGCTGGCGGTGGTGACCGGTACCTATCTGCTGGCAGTGGAAAGCGAC
    ACCGCCGCCATCGTCGCGTTCGTCTTCGCCGGGGTGATCACCTGCGCGATGGGGGCCATT
    CCATGGGTGACGCTCAAGAAGCTGCGCGAGCTCGGCTCGTCGGGGTCTTAG 

    After I perform a local BLAST, how can I get something like the following?


    PHP Code:
    >final_001_R1_00001 hypothetical protein
    ATGCCAGCAGGTCGATTGGCCAAGCCACTGGAGGCAATCGCGGGCCCGCTGCGGCGGTCA
    TCGCCGGAGTCCGTTGACCGGATGCTCATCGGCTTGTGCGCGGTCATCTGGTTGGCGTTC
    GTCGGGATGCTGGTCGGTGCCATCGTGGTGATCGCCGGAATGGGGGAGGACTCGGGTTCG
    TCGGGGTCTTCGTGGGGCATCTACATCGTCATCGGGGTATCGCTGGCCGTCATCGTCGGT
    GCCGTGCCGCTGTTGCTACGTGCCCGCAACACCGCTGCCCAGCGCACCTCGAAAACGGCC
    CCTAAAACCAAGGGCGCCAATTCCTCCGGTGGGGCCACTGCGCCGTCTGGACCGCCTCCC
    GCGGAGGCGTCGACCGAGAAGCTCAAGACCTTCGGTGGTCTCGCCGATCACGTGAGCCAT
    GTTCCCAAGGACTACAACGGTCCTGGGTCACCCGCGTACCGGGCAGCCACCGAGGCGGCC
    GCGAAGAGGGCGGTGGTCAACCGGCTGTGGTTGCGGGCCACGGTGGGGATCGCCGGCGCG
    ATCGGCCTGGCACTGCTGGCGGTGGTGACCGGTACCTATCTGCTGGCAGTGGAAAGCGAC
    ACCGCCGCCATCGTCGCGTTCGTCTTCGCCGGGGTGATCACCTGCGCGATGGGGGCCATT
    CCATGGGTGACGCTCAAGAAGCTGCGCGAGCTCGGCTCGTCGGGGTCTTAG 
    In other words, after performing gene prediction, how to get a file which project the sequences as following?

    PHP Code:
    >gene_0001 GENE_NAME_A
    SEQUENCE    ...
    >    gene_0002 GENE_NAME_B
    SEQUENCE    ...
    >    gene_0003 GENE_NAME_C
    SEQUENCE    ...
    >    gene_0004 GENE_NAME_D
    SEQUENCE    ...
    >    gene_0005 GENE_NAME_E
    SEQUENCE    ...
    >    gene_0006 GENE_NAME_F
    SEQUENCE    ... 
    Tags: None
    • Desai
      Member
      • Dec 2013
      • 18
      #2
      Dear garethboy

      I dont't know how to get sequence like that but yes u can use BLAST2GO tool for mapping and annotation. could I know what is your conclusion?

        Comment

        • boetsie
          Senior Member
          • Feb 2010
          • 245
          #3
          Use a tool like Prokka (http://www.vicbioinformatics.com/software.prokka.shtml) to predict and annotate your sequences. After the genbank or other files are generated, write a script to add the annotation to your fastA file.

          Boetsie

            Comment

            Previous template Next

            Latest Articles

            Collapse
            • SEQadmin2
              Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
              by SEQadmin2



              Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

              Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating              ...
              10-14-2026, 09:55 AM
            • SEQadmin2
              New Genomics Technologies Take Aim at Long-Standing Limits
              by SEQadmin2


              Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

              We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing              ...
              09-28-2026, 10:25 AM
            View All

            ad_right_rmr

            Collapse

            News

            Collapse
            Topics Statistics Last Post
            Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
            Started by SEQadmin2, 10-22-2026, 11:13 AM
            0 responses
            28 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            10-22-2026, 11:13 AM  
            Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2
            Started by SEQadmin2, 10-22-2026, 10:48 AM
            0 responses
            20 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            10-22-2026, 10:48 AM  
            Mayo Clinic-Led Study Detects DNA Mutations Across Noncancerous Tissues by SEQadmin2
            Started by SEQadmin2, 10-15-2026, 10:52 AM
            0 responses
            38 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            10-15-2026, 10:52 AM  
            Study Finds Chromatin Motion Holds Steady Until Cells Face Stress by SEQadmin2
            Started by SEQadmin2, 10-14-2026, 05:39 AM
            0 responses
            44 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            10-14-2026, 05:39 AM  
            View All
            Working...