So, I am new to bioinformatics. we have been provided with a task and there was very little guidance and as I am new to this I am finding this really difficult. I am provided with two fastq files of hbb and cdk3 - nucleotide sequences- both the files are subsamplednto only contain reads that align to cdk3 and hbb. first task was to convert the fast q files into fasta files. I did it using galaxy. now I am asked to perform multiple sequence alignment on those reads. both the files have like 30 reads and to highlight on the alignment any difference between the proband and the refernce sequence.
I have not been provided with any other files. so should I get the reference file from ncbi or should I use blast. also when using blast should I upload all 30 reads or only 4 or 5. and how to do multiple sequence alignment and understand the differences. I am doing something and getting outputs but I am not sure if it is right.
Any thoughts on how to do this will very much be appreciated.
Thank you
This sounds an awful lot like homework. Is it?
BLAST is not an MSA tool. It's a database searching tool, though it can emit an MSA of results. Use a dedicated MSA tool, there are many, all of which can easily be found using google. Based on your description, I would download a reference from somewhere like NCBI and include it in the MSA.
computer was not in my subjects since high school, so this is really difficult for me. thank you for the reply. so if im doing MSA using clustal omega, do i just use 4 or 5 reads of the given gene sequences and all of the reference sequence? and how do i find the variants from it?
I'm going to take that as a yes re' homework. We generally try not to offer answers to homework since you don't learn if we do. That said, only adding 4-5 reads to the MSA is only making more work for yourself. Good luck.