Regarding Whole Genome Visualization
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5.6 years ago

Hi, I want to visualize the whole genome, but I have Multi fasta sequence file (contigs) and it has been accepted by the NCBI. The multi fasta sequence file contains contigs in a random order. So,can I just remove the fasta headers (by sequence massager tool ), stich up all the fasta sequences and use it for whole genome visualisation?

Is it a correct thing to do???

genome • 1.9k views
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Whole genome visualization? Visualization of what? Do you have any example plot you want to create with your data?

can I just remove the fasta headers (by sequence massager tool ), stich up all the fasta sequences and use it for whole genome visualisation?

I didn't understand what you want to do but I would certainly say this is not a good idea for any type of problem (except to find percentage of each nt in all fasta sequences combined.)

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Actually, my genome contains multiple contigs and they are in random fashion. first sequence is contig no. 1, and second one is contig no.10, and the third one is contig no. 3. and so on...

So, now if I have to blast it with the Anti microbial resistance genes database,just to avoid multiple hits with same sequence, Can I delete all the fasta headers of contigs and convert it into one single fasta sequence? So that it will be helpful for me to find the particular gene in the given coordinates. Is it advisable ?

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Entering edit mode
5.3 years ago
Joe 20k

If you want to de-randomise them you can re-order the contigs via Mauve if you have a reference sequence for the organism available.

The only other thing you can do is try to scaffold the contigs, which will attempt to order them and then join the sequences with N for regions not represented in your sequencing.

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5.3 years ago
ThulasiS ▴ 90

I suggest you to use MAUVE for visualization of your contigs and part from that have a look at CCT-view for whole genome visualization. Refer: J.R. Grant, A.S. Arantes, P. Stothard, “Comparing thousands of circular genomes using the CGView Comparison Tool” BMC Genomics 13, 202, 2012. It may help you.