I have whole genome sequence data for a mutant. I wish to align a gene sequence to the whole genome sequence to check for potential SNPs. Clustal W fails to upload the sequence properly. I have downloaded Clustal W, that also crashes when I try to load the whole genome sequence as a profile in pair wise alignment.
I have also tried multiple sequence alignemnt tools on EBI. They took forever to load the genome sequence.
My genome sequence is a paired-end sequence. I had concatenated both reads on Galaxy and am using FASTA file of the concatenated reads.
Is there a mistake in what I am doing? Can anyone suggest me any other way?
Thanks.
Maybe you can try BWA (http://bio-bwa.sourceforge.net/) or Bowtie (http://bowtie-bio.sourceforge.net/manual.shtml).
It works well for my SNPs detection in RADseq
First, I have some questions about your genome sequence.
Is it properly assembled with assemble tools? You mentioned that your paired end sequence was concatenated in Galaxy. Which tools was used in Galaxy platform?
In genome scale, generally webtools are not enough for alignment because of resource limitation.
As Dorant says, BWA aligner of Bowtie can be good solution for mapping a gene sequence.
I found that two tools are equipped in Galaxy platform.
Dear Sravanthi,
Based on your description, I think you have not assembled your sequence data. To begin with, you should perform de novo assembly on your raw sequence reads using SPades assembler for example with careful option (Galaxy might have this tool available). Once you have your draft genome, you can then perform a blastn alignment of your gene of interest to identify for the presence of any variant nucleotides. Hope that helps.
I have used Pear to merge my paired-end reads together.
I think I go with your suggestion and try assembling my reads again.
Thank you all.
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