Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • About tools for comparing genomes of two different organisms

    Hi Bioinformatics gurus,

    Could you suggest me any tool(s) for comparing genomes of two (or more) different organisms to have at the end a list of genes of organism A which are lacking in organism B? And also, a list of common genes in both organisms which are drastically different.

    Thanks

  • #2
    Maybe InParanoid http://www.ncbi.nlm.nih.gov/pubmed/19892828 can help you? From the documentation http://inparanoid.sbc.su.se/download...t/relnotes.txt

    1. Introduction

    InParanoid is a program for automatic identification of orthologs
    while differentiating between inparalogs and outparalogs. An
    InParanoid cluster is seeded by a reciprocally bestmatching ortholog
    pair, around which inparalogs are gathered independently, while
    outparalogs are excluded. The InParanoid database is a collection of
    pairwise ortholog groups aiming to include all 'completely sequenced'
    eukaryotic genomes. By this we mean above 6X coverage, and less than
    1% X letters in the protein sequences.

    Comment


    • #3
      Hi,
      I'm assuming they've been annotated and are bacteria/virus.
      You can use MAUVE, which can do the alignment of 2 or more genomes and there is an option output orthologues based on your cutoffs. The output is a table (which can be opened in excel), where across the top (X axis) are the organism name, below which are the genes present. Comparing the columns, you can pull out whats shared and whats not.

      Alternatively, you could you Blast to compare and pull out similar sequences between the genomes, again using what ever cutoff you like - that can be the more labour intensive way and gets complicated with 3 or more genomes.

      Cheers,
      Raj

      Comment


      • #4
        A clutering tool like cd-hit would work.

        Comment


        • #5
          No second dariober's suggestion to use InParanoid. Its summary information and definitions of orthologs vs paralogs is quite useful. The key is that you must have annotated organisms to start with. And keep in mind the most likely differences are going to arise from genome assembly errors. For example my first pass filter on gene loss is to run peptide BLAT/BLAST and look for hits on the *_random chromosomes. I'd often find fragments of the gene at the edges of genome gaps. Sometimes half the gene would be on chr6, the other half on chr6_random, but you could see pretty much anything, depending upon the quality of the assembly and the annotation. But InParanoid should in theory help you figure out what to follow up with a deeper analysis, ie what holes there are to fill.

          Comment


          • #6
            Hi, I'm facing the same kind of situation. Anybody here used InParanoid successfully?

            Comment


            • #7
              Muave generates visual comparisons for genomes.

              BTW: Are you not able to make InParanoid work?

              Comment


              • #8
                Thanks GenoMax, I'm now trying Mauve. As for InParanoid, I'm not able to make it work on my transcriptomes. It's working with a small subset of sequences (a few thousands sequences) but it freezes forever when I try with the whole transcriptomes (hundreds of thousands sequences).

                Comment

                Latest Articles

                Collapse

                • 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
                • seqadmin
                  Multiomics Techniques Advancing Disease Research
                  by seqadmin


                  New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

                  A major leap in the field has
                  ...
                  02-08-2024, 06:33 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, Today, 06:12 AM
                0 responses
                13 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 02-23-2024, 04:11 PM
                0 responses
                67 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 02-21-2024, 08:52 AM
                0 responses
                70 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 02-20-2024, 08:57 AM
                0 responses
                61 views
                0 likes
                Last Post seqadmin  
                Working...
                X